Alignments for a candidate for prpE in Arenitalea lutea P7-3-5

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Arenitalea lutea P7-3-5

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_019387229.1 P735_RS0106605 acetate--CoA ligase

Query= reanno::Phaeo:GFF1175
         (629 letters)



>NCBI__GCF_000283015.1:WP_019387229.1
          Length = 632

 Score =  693 bits (1788), Expect = 0.0
 Identities = 333/618 (53%), Positives = 431/618 (69%)

Query: 1   MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60
           M+Y E Y+    +PEQFW + A+ + W  +P   L+      ++WF D ++N  Y  +D+
Sbjct: 1   MNYQEFYQNSLKHPEQFWSQQAQELEWFKSPKIILSKDKHDYFQWFEDGQLNLSYLCIDK 60

Query: 61  HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120
           H++ G GEQ AIIYDSP+T+ K+ IS+ +L   V+ LAG L++ G+E+GD  IIYMPMIP
Sbjct: 61  HIKDGFGEQDAIIYDSPVTNAKKHISFNQLHFEVSKLAGGLQSLGLERGDTCIIYMPMIP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180
           +A+ AMLAC R+G +HSVVFGGFA +ELA+RIDD  PKAII AS G+E  + + YKP +D
Sbjct: 121 QAIYAMLACVRIGVIHSVVFGGFAPHELAIRIDDCKPKAIITASNGIEIEKIIPYKPFVD 180

Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
            AI  A +KP+  V+F R+  V    +  D+++          + V VE  HP+YILYTS
Sbjct: 181 EAITKAENKPEHVVVFDRQLGVEIPKKNYDIDYKSLVENSPSVDAVSVESIHPSYILYTS 240

Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTG PKG+IR T G   AL ++MK +Y VD GD FWAASDVGWVVGHSYI YGPL++ N
Sbjct: 241 GTTGTPKGIIRDTGGYATALKFSMKYVYGVDEGDTFWAASDVGWVVGHSYIVYGPLLNRN 300

Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360
           TTI+FEGKPI TPDA TFWRVISEH VK  FTAPTA RA+K+EDP G  +K++D+SCLK 
Sbjct: 301 TTILFEGKPIRTPDASTFWRVISEHNVKVMFTAPTAIRAIKKEDPTGHMIKRFDMSCLKY 360

Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420
            +LAGER D  T+ W  E+L VPVIDHWWQTE+GW + AN +G+E    K GS + P+ G
Sbjct: 361 QFLAGERCDVATLNWTHEKLNVPVIDHWWQTESGWPMLANMVGVELQEVKPGSASFPVCG 420

Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480
           Y + IL+E G  V     G +AVKLPLPPGTL  LW    RFK  YL  FPGYY +GD G
Sbjct: 421 YDIKILNEAGEEVEASVEGYVAVKLPLPPGTLSNLWGNPKRFKSGYLERFPGYYFSGDGG 480

Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540
            KDED Y++I  R DD+INVAGHRLST  MEE++A +  VAECAV GV   +KGQ P+G 
Sbjct: 481 YKDEDDYVFITGRVDDIINVAGHRLSTAEMEEIVASNKVVAECAVFGVHCEIKGQKPLGL 540

Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600
           + L +  D+ +  +  +++K VR +IG VA+FK   +V+RLPKTRSGKILR  + NIAD 
Sbjct: 541 IVLKSNVDSDNSQIQKEIIKDVRNEIGAVASFKDVLIVNRLPKTRSGKILRKLLRNIADE 600

Query: 601 TDWKMPATIDDPAILDEI 618
             + +P+TIDD AI++EI
Sbjct: 601 RQYNIPSTIDDVAIINEI 618


Lambda     K      H
   0.318    0.137    0.428 

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: 1179
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: 629
Length of database: 632
Length adjustment: 38
Effective length of query: 591
Effective length of database: 594
Effective search space:   351054
Effective search space used:   351054
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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