GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Azoarcus olearius BH72

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011766904.1 AZO_RS15950 propionate--CoA ligase

Query= BRENDA::P77495
         (628 letters)



>NCBI__GCF_000061505.1:WP_011766904.1
          Length = 630

 Score =  792 bits (2045), Expect = 0.0
 Identities = 380/627 (60%), Positives = 484/627 (77%), Gaps = 3/627 (0%)

Query: 2   SFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRW 61
           ++ EF++RSI++ ++FWAEQA+ +DW  P  Q  D S PPF +WF  G TNLC+NA+DR 
Sbjct: 3   NYKEFHRRSIDQRDEFWAEQAQLVDWHKPAEQICDFSKPPFVKWFKGGETNLCYNAVDRH 62

Query: 62  LEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEA 121
             K+P+  AL+ +S+ET EE+ ++F +L  EV  +A++ + LGV+RGDRVL+YMPMIAEA
Sbjct: 63  AAKRPDDRALVYISTETNEEKVYSFAELQREVERMAAIYQDLGVKRGDRVLIYMPMIAEA 122

Query: 122 HITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDA 181
              +LACARIGAIHSVVFGGFA+ S+A RIDDAKPVL+VS+DAG R GK +PYK L+D+A
Sbjct: 123 AFAMLACARIGAIHSVVFGGFAAGSLATRIDDAKPVLMVSSDAGMRNGKPVPYKHLVDEA 182

Query: 182 ISQAQHQPRHVLLVDRGLAK-MARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240
              A+  P  VL+VDRGL K   +V  RDVD+A LR +HI A+VPV WLES+E S ILYT
Sbjct: 183 CKLAEFPPAKVLIVDRGLDKGFPKVESRDVDYAELRAKHIDAKVPVTWLESSEPSYILYT 242

Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300
           SGTTGKPKGVQRD GGY VALA SM  IF G +G   F  SDIGWVVGHSYI+Y PL+AG
Sbjct: 243 SGTTGKPKGVQRDTGGYTVALAASMKHIFTGGSGETMFSTSDIGWVVGHSYIIYGPLIAG 302

Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360
           MATI+YEG P  PD G+WW IVEKY+VS MFSAPTA+RVLKK   A ++K+DLSSL+ L+
Sbjct: 303 MATIMYEGTPLRPDAGIWWQIVEKYKVSVMFSAPTAVRVLKKQDPAFLKKYDLSSLKHLF 362

Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420
           LAGEPLDE +  W+ + L +PVIDNYWQTE+GWP++AI RG++D   +LGSP  P+YGY+
Sbjct: 363 LAGEPLDETSHKWIMSELGIPVIDNYWQTETGWPMLAIVRGVEDSKIKLGSPAFPVYGYD 422

Query: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRP-VYATFDW 479
           +++  E  G  CG NEKG++ +  PLPPGC+ T+WG D RFV TY+SLF+ P VY++ DW
Sbjct: 423 LRIFRE-DGSECGPNEKGIVGIVPPLPPGCLSTVWGQDERFVSTYFSLFTDPVVYSSSDW 481

Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
           GI+D +GYH ILGR DDVINVAGHRLGTREIEE++ +HP +AEVAVVGV D LKGQ+ +A
Sbjct: 482 GIKDENGYHTILGRMDDVINVAGHRLGTREIEEAVQTHPAIAEVAVVGVHDELKGQMPMA 541

Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
           F + K++ +++  +   + EK +M  VD  +G   RPA V F++ LPKTRSGKMLRR+IQ
Sbjct: 542 FAVVKDASTVDTAEKRAALEKEVMKKVDESLGAIARPARVHFINGLPKTRSGKMLRRSIQ 601

Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAM 626
           A+ EGRD GDLTTIDDP +LDQI+ A+
Sbjct: 602 ALAEGRDAGDLTTIDDPTTLDQIKAAL 628


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: 1206
Number of extensions: 41
Number of successful extensions: 4
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 WP_011766904.1 AZO_RS15950 (propionate--CoA ligase)
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.aa/TIGR02316.hmm
# target sequence database:        /tmp/gapView.3517763.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 1078.5   0.1          0 1078.2   0.1    1.0  1  NCBI__GCF_000061505.1:WP_011766904.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000061505.1:WP_011766904.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1078.2   0.1         0         0       2     626 ..       3     628 ..       2     630 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1078.2 bits;  conditional E-value: 0
                             TIGR02316   2 ayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalvav 74 
                                           +y+e+++rsi++ ++fwaeqa+ +dw+ p +++ d s++pf +wf gg+tnlcynavdrh +kr+++ alv++
  NCBI__GCF_000061505.1:WP_011766904.1   3 NYKEFHRRSIDQRDEFWAEQAQLVDWHKPAEQICDFSKPPFVKWFKGGETNLCYNAVDRHAAKRPDDRALVYI 75 
                                           69*********************************************************************** PP

                             TIGR02316  75 ssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashsl 147
                                           s+et+ee+ +++ +l rev+++a++ + lgv+rgdrvliy+pmiaeaa+a+lacarigaihsvvfggfa+ sl
  NCBI__GCF_000061505.1:WP_011766904.1  76 STETNEEKVYSFAELQREVERMAAIYQDLGVKRGDRVLIYMPMIAEAAFAMLACARIGAIHSVVFGGFAAGSL 148
                                           ************************************************************************* PP

                             TIGR02316 148 aariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglak.lrrvpgrdvdyaalrrqh 219
                                           a+ridda+p+l+vs+dag+r gk ++yk+l+d+a++ a  +pa+vl+vdrgl+k + +v +rdvdya lr +h
  NCBI__GCF_000061505.1:WP_011766904.1 149 ATRIDDAKPVLMVSSDAGMRNGKPVPYKHLVDEACKLAEFPPAKVLIVDRGLDKgFPKVESRDVDYAELRAKH 221
                                           ******************************************************99***************** PP

                             TIGR02316 220 edadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyi 292
                                           +da+v+v wles+epsyilytsgttgkpkgvqrd+ggy+valaasm+ if + +g+++fs+sd+gwvvghsyi
  NCBI__GCF_000061505.1:WP_011766904.1 222 IDAKVPVTWLESSEPSYILYTSGTTGKPKGVQRDTGGYTVALAASMKHIFTGGSGETMFSTSDIGWVVGHSYI 294
                                           ************************************************************************* PP

                             TIGR02316 293 vyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagep 365
                                           +y+pl+ag+at++yeg+p rpd+g+ww+iveky+vsvmfsapta+rvlkkqd+a l+k+dlssl++lflagep
  NCBI__GCF_000061505.1:WP_011766904.1 295 IYGPLIAGMATIMYEGTPLRPDAGIWWQIVEKYKVSVMFSAPTAVRVLKKQDPAFLKKYDLSSLKHLFLAGEP 367
                                           ************************************************************************* PP

                             TIGR02316 366 ldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvygyrldvldeatgedvgpnekg 438
                                           lde + +wi   lg pvidnywqtetgwp+lai+rg++d+  klgsp +pvygy+l+++ e  g ++gpnekg
  NCBI__GCF_000061505.1:WP_011766904.1 368 LDETSHKWIMSELGIPVIDNYWQTETGWPMLAIVRGVEDSKIKLGSPAFPVYGYDLRIFRE-DGSECGPNEKG 439
                                           ***********************************************************99.699******** PP

                             TIGR02316 439 llvvaaplppgclstvwgddarflktyfsafkrl.lyssldwgirdedgytfilgrtddvinvaghrlgtrei 510
                                           ++ +++plppgclstvwg+d rf+ tyfs+f+++ +yss dwgi+de+gy++ilgr ddvinvaghrlgtrei
  NCBI__GCF_000061505.1:WP_011766904.1 440 IVGIVPPLPPGCLSTVWGQDERFVSTYFSLFTDPvVYSSSDWGIKDENGYHTILGRMDDVINVAGHRLGTREI 512
                                           ********************************6527************************************* PP

                             TIGR02316 511 eesvsshaavaevavvgvkdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarparvyvva 583
                                           ee+v +h+a+aevavvgv+delkgq+++afa++k+a++v+ a+++ aleke+m+ v++ lga+arparv++++
  NCBI__GCF_000061505.1:WP_011766904.1 513 EEAVQTHPAIAEVAVVGVHDELKGQMPMAFAVVKDASTVDTAEKRAALEKEVMKKVDESLGAIARPARVHFIN 585
                                           ************************************************************************* PP

                             TIGR02316 584 alpktrsgkllrraiqavaegrdpgdlttiddpaaleqvreal 626
                                            lpktrsgk+lrr+iqa+aegrd gdlttiddp++l+q++ al
  NCBI__GCF_000061505.1:WP_011766904.1 586 GLPKTRSGKMLRRSIQALAEGRDAGDLTTIDDPTTLDQIKAAL 628
                                           ****************************************998 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 32.74
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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