Alignments for a candidate for prpE in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Cupriavidus basilensis 4G11

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate RR42_RS13560 RR42_RS13560 propionyl-CoA synthetase

Query= BRENDA::P77495
         (628 letters)



>FitnessBrowser__Cup4G11:RR42_RS13560
          Length = 630

 Score =  830 bits (2145), Expect = 0.0
 Identities = 402/622 (64%), Positives = 493/622 (79%), Gaps = 1/622 (0%)

Query: 7   YQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRWLEKQP 66
           + RS+++PE FWAEQARRIDW+TPF   LD S PPF RWF  GRTNLCHNA+DR L ++ 
Sbjct: 8   HARSLSDPEGFWAEQARRIDWETPFDTVLDDSRPPFTRWFVGGRTNLCHNAVDRHLAERA 67

Query: 67  EALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEAHITLL 126
           +  ALI VS+ET + RT+++ +LHDEVN +A++L+ LGV +GDRVL+YMPMI EA   +L
Sbjct: 68  DQAALIYVSTETGQHRTYSYAELHDEVNRMAAILQQLGVVKGDRVLIYMPMIPEAAFAML 127

Query: 127 ACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDAISQAQ 186
           ACARIGAIHSVVFGGFAS S+AARIDDA+P +IVSADAG+R GK++PYK LLD+A+  A 
Sbjct: 128 ACARIGAIHSVVFGGFASVSLAARIDDAQPRVIVSADAGSRAGKVVPYKPLLDEAVKLAT 187

Query: 187 HQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYTSGTTGK 246
           H+P  VLLVDR L+ M    GRD D+ + R +   ARVP AWLES+E S +LYTSGTTGK
Sbjct: 188 HKPERVLLVDRQLSPMTLTPGRDEDYGAWRERVGAARVPCAWLESSEPSYVLYTSGTTGK 247

Query: 247 PKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAGMATIVY 306
           PKGVQRD GGYAVALA SM+ IF GKAG   F +SDIGWVVGHSYI+Y PLLAGMATI+Y
Sbjct: 248 PKGVQRDTGGYAVALAASMEYIFCGKAGDTMFSSSDIGWVVGHSYIIYGPLLAGMATIMY 307

Query: 307 EGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLYLAGEPL 366
           EG P  PD G+ W +VE+Y V+ MFSAPTAIRVLKK   A + ++DLSSL +L+LAGEPL
Sbjct: 308 EGTPIRPDGGILWQLVEQYHVNIMFSAPTAIRVLKKQDPAWLTRYDLSSLRLLFLAGEPL 367

Query: 367 DEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYNVQLLNE 426
           DEPTASW+   +  PV+DNYWQTE+GWPI+AI RGLD  P +LGSPGVP+YGY++++++E
Sbjct: 368 DEPTASWIQQGIGKPVVDNYWQTETGWPIIAIQRGLDPLPAKLGSPGVPVYGYDLKIIDE 427

Query: 427 VTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWS-LFSRPVYATFDWGIRDAD 485
            TG  C   +KG++ ++GPLPPGC+ T+WGDD RFVKTYWS +  R  Y+TFDWG++D D
Sbjct: 428 ATGAECPPGQKGVVAIDGPLPPGCMTTVWGDDERFVKTYWSGVPGRRCYSTFDWGVQDED 487

Query: 486 GYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAFVIPKE 545
           GY FILGRTDDVINVAGHRLGTREIEESISSHP VAEVAVVGV DALKGQ A+AFVI ++
Sbjct: 488 GYIFILGRTDDVINVAGHRLGTREIEESISSHPAVAEVAVVGVHDALKGQAAMAFVIVRD 547

Query: 546 SDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQAICEGR 605
           +     +      E  +M  VD Q+G   RPA V+FV+ LPKTRSGK+LRR +QA+ EGR
Sbjct: 548 AGRTATQADRLVLEGDVMKTVDQQLGAVARPARVFFVNALPKTRSGKLLRRAMQAVAEGR 607

Query: 606 DPGDLTTIDDPASLDQIRQAME 627
           DPGDLTTI+DP +L Q++ AM+
Sbjct: 608 DPGDLTTIEDPTALAQLQAAMQ 629


Lambda     K      H
   0.320    0.136    0.422 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1244
Number of extensions: 46
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 628
Length of database: 630
Length adjustment: 38
Effective length of query: 590
Effective length of database: 592
Effective search space:   349280
Effective search space used:   349280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate RR42_RS13560 RR42_RS13560 (propionyl-CoA synthetase)
to HMM TIGR02316 (prpE: propionate--CoA ligase (EC 6.2.1.17))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02316.hmm
# target sequence database:        /tmp/gapView.28852.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02316  [M=628]
Accession:   TIGR02316
Description: propion_prpE: propionate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1150.0   0.8          0 1149.8   0.8    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS13560  RR42_RS13560 propionyl-CoA synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS13560  RR42_RS13560 propionyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1149.8   0.8         0         0       4     627 ..       5     629 ..       2     630 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1149.8 bits;  conditional E-value: 0
                                 TIGR02316   4 eelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalv 72 
                                               ++l+ rs+ +pe fwaeqarridw+tpf +vldds++pf+rwfvggrtnlc+navdrhl++r++q+al+
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560   5 RALHARSLSDPEGFWAEQARRIDWETPFDTVLDDSRPPFTRWFVGGRTNLCHNAVDRHLAERADQAALI 73 
                                               799****************************************************************** PP

                                 TIGR02316  73 avssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfgg 141
                                               +vs+etg++rt++y +lh+evn++a++l+ lgv +gdrvliy+pmi+eaa+a+lacarigaihsvvfgg
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560  74 YVSTETGQHRTYSYAELHDEVNRMAAILQQLGVVKGDRVLIYMPMIPEAAFAMLACARIGAIHSVVFGG 142
                                               ********************************************************************* PP

                                 TIGR02316 142 fashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglaklrrvpgrdv 210
                                               fas slaaridda+p++ivsadag+r gkv++yk+lld+a++ a hkp+ vllvdr+l++++ +pgrd 
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 143 FASVSLAARIDDAQPRVIVSADAGSRAGKVVPYKPLLDEAVKLATHKPERVLLVDRQLSPMTLTPGRDE 211
                                               ********************************************************************* PP

                                 TIGR02316 211 dyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfs 279
                                               dy a r++   a+v+++wles+epsy+lytsgttgkpkgvqrd+ggyavalaasm+ if +kagd++fs
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 212 DYGAWRERVGAARVPCAWLESSEPSYVLYTSGTTGKPKGVQRDTGGYAVALAASMEYIFCGKAGDTMFS 280
                                               ********************************************************************* PP

                                 TIGR02316 280 asdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqdaall 348
                                               +sd+gwvvghsyi+y+pllag+at++yeg+p+rpdgg+ w++ve+y+v+ mfsaptairvlkkqd+a+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 281 SSDIGWVVGHSYIIYGPLLAGMATIMYEGTPIRPDGGILWQLVEQYHVNIMFSAPTAIRVLKKQDPAWL 349
                                               ********************************************************************* PP

                                 TIGR02316 349 rkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvy 417
                                                ++dlssl+ lflagepldepta+wi +++gkpv+dnywqtetgwp++ai+rgld+ p+klgspg+pvy
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 350 TRYDLSSLRLLFLAGEPLDEPTASWIQQGIGKPVVDNYWQTETGWPIIAIQRGLDPLPAKLGSPGVPVY 418
                                               ********************************************************************* PP

                                 TIGR02316 418 gyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafk.rllyssldwgirded 485
                                               gy+l+++deatg ++ p++kg++++ +plppgc++tvwgdd rf+kty+s  + r  ys++dwg++ded
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 419 GYDLKIIDEATGAECPPGQKGVVAIDGPLPPGCMTTVWGDDERFVKTYWSGVPgRRCYSTFDWGVQDED 487
                                               ****************************************************99*************** PP

                                 TIGR02316 486 gytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsvedadd 554
                                               gy+filgrtddvinvaghrlgtreiees+ssh+avaevavvgv+d+lkgq a+af+i+++a + + ++d
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 488 GYIFILGRTDDVINVAGHRLGTREIEESISSHPAVAEVAVVGVHDALKGQAAMAFVIVRDAGRTATQAD 556
                                               ********************************************************************* PP

                                 TIGR02316 555 ahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaaleqvr 623
                                               +  le+++m++v++qlgavarparv++v+alpktrsgkllrra+qavaegrdpgdltti+dp+al+q++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 557 RLVLEGDVMKTVDQQLGAVARPARVFFVNALPKTRSGKLLRRAMQAVAEGRDPGDLTTIEDPTALAQLQ 625
                                               ********************************************************************* PP

                                 TIGR02316 624 eale 627
                                                a++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13560 626 AAMQ 629
                                               **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (630 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.07
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources