GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Desulfovibrio vulgaris Hildenborough

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  486 bits (1251), Expect = e-141
 Identities = 247/512 (48%), Positives = 325/512 (63%)

Query: 2   LQPYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61
           L P+ ++   DFTV  NRKAF EAL  V    G+  PL I G  VTT D I + NPA+  
Sbjct: 477 LPPFTNDAMIDFTVPDNRKAFVEALADVRSRFGQTVPLYIGGRDVTTADLIPTTNPAKPA 536

Query: 62  QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121
           ++V S+ +A +   + AI +A +A  TWR+ +P +RA  L +AA I R+R  E SAW V 
Sbjct: 537 EVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADRAAYLRRAADICRKRIWELSAWQVV 596

Query: 122 EAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPW 181
           E GK W +A  D  E IDFLEYYAR+M+ L   + +   PGE N  FY P G+   I+PW
Sbjct: 597 EVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEHNHLFYQPKGIAAVIAPW 656

Query: 182 NFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEV 241
           NF  AI +G A A IVTGN V+ KP+S +  +     EV  +AGLP+GV NY PG  + +
Sbjct: 657 NFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIM 716

Query: 242 GDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADL 301
           GDYLV+HP  SLI FTGS +VG+R+ E+AA V+PGQ   KRVI EMGGK+  ++D DADL
Sbjct: 717 GDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADL 776

Query: 302 DLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGP 361
           D A   +L SAFGF GQKCSA SR ++   +YD  +E+ V  A ++ +G   +  NYMGP
Sbjct: 777 DEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGP 836

Query: 362 VIDEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPV 421
           V D    + +  YI I ++EGR++       + G ++  TI+ D+ PE  I QEEIFGPV
Sbjct: 837 VADATLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGPV 896

Query: 422 VAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGY 481
           +A  +A  FD AL IAN T + LTGAV +R+  H+++A+REF VGNLY N+  TGA+V  
Sbjct: 897 LAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVER 956

Query: 482 HPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
            PFGGF MSG  SK GGPDYL   M  + V+E
Sbjct: 957 QPFGGFAMSGVGSKTGGPDYLLQFMDPRVVTE 988


Lambda     K      H
   0.316    0.134    0.388 

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: 1188
Number of extensions: 45
Number of successful extensions: 1
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: 515
Length of database: 1006
Length adjustment: 40
Effective length of query: 475
Effective length of database: 966
Effective search space:   458850
Effective search space used:   458850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate 208845 DVU3319 (proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01237 (pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01237.hmm
# target sequence database:        /tmp/gapView.25084.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01237  [M=511]
Accession:   TIGR01237
Description: D1pyr5carbox2: putative delta-1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-204  666.7   0.0   1.6e-204  666.4   0.0    1.1  1  lcl|MicrobesOnline__882:208845  DVU3319 proline dehydrogenase/de


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208845  DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.4   0.0  1.6e-204  1.6e-204       3     510 ..     482     989 ..     480     990 .. 0.99

  Alignments for each domain:
  == domain 1  score: 666.4 bits;  conditional E-value: 1.6e-204
                       TIGR01237   3 nepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeqalqaakka 81 
                                     n+   df+  ++++af +ala v+  +G++ pl+i G+ v t++ i + npa++ evv  +++a   + ++a+ aakka
  lcl|MicrobesOnline__882:208845 482 NDAMIDFTVPDNRKAFVEALADVRSRFGQTVPLYIGGRDVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKA 560
                                     67788************************************************************************** PP

                       TIGR01237  82 feewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremiklakskevlsieGek 160
                                       +w+ t++ +raa l++aa+i ++r  elsa+ v+evGk++++a  +v+e idfleyyarem++l   +     +Ge+
  lcl|MicrobesOnline__882:208845 561 ALTWRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEH 639
                                     ******************************************************************************* PP

                       TIGR01237 161 nrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveileeaGlpkGvlqfvpGkGsevGe 239
                                     n+++y+p+G+a vi+pwnfp+ai++Gm+ a+ivtGn v+ kp++ ++ i   l+e+++eaGlp+Gv+++ pG+ s +G+
  lcl|MicrobesOnline__882:208845 640 NHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIMGD 718
                                     ******************************************************************************* PP

                       TIGR01237 240 ylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivdesadieqavaaavtsafGfaGqkcsa 318
                                     ylv+hp+++li+ftGs evGlri e+aakvqpGq+  krviae+GGk+a i+d++ad+++av  +++safGf+Gqkcsa
  lcl|MicrobesOnline__882:208845 719 YLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSA 797
                                     ******************************************************************************* PP

                       TIGR01237 319 asrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikpt 397
                                     +srv+vl+ +yd+++er+v+a+ s ++g++++++ ++gpv d++ ++++ +yi ++++eg+++l  +d + +G ++  t
  lcl|MicrobesOnline__882:208845 798 CSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCYVPLT 876
                                     ******************************************************************************* PP

                       TIGR01237 398 ifkdvdrkarlaqeeifGpvvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivg 476
                                     i++d+ ++ r+aqeeifGpv+av+ra+ fdeal ian+t ++ltG+v+s+s+e++++a+ ef+vGnly+n+  tGa+v 
  lcl|MicrobesOnline__882:208845 877 IVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVE 955
                                     ******************************************************************************* PP

                       TIGR01237 477 vqpfGGfkmsGtdskaGGpdylaqflqaktvter 510
                                     +qpfGGf msG++sk+GGpdyl+qf++++ vte+
  lcl|MicrobesOnline__882:208845 956 RQPFGGFAMSGVGSKTGGPDYLLQFMDPRVVTEN 989
                                     ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (1006 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 19.09
//
[ok]

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

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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:

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:

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:

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:

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