Alignments for a candidate for paaH in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Thiothrix lacustris DSM 21227

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_028489632.1 Q394_RS0112850 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000621325.1:WP_028489632.1
          Length = 774

 Score =  549 bits (1415), Expect = e-160
 Identities = 315/794 (39%), Positives = 465/794 (58%), Gaps = 29/794 (3%)

Query: 4   HIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSR 63
           +I K AV+G+GVMG+GIAAH+AN GIPVLLLDIVP              + +  RS+++ 
Sbjct: 2   NIHKVAVIGAGVMGAGIAAHIANAGIPVLLLDIVP--------------EGASDRSQIAN 47

Query: 64  QAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVD 123
            A+ KLLK  PAP    KN   +TPGN+EDD  +L + DWIIE +VE L +K+ ++  + 
Sbjct: 48  TALAKLLKADPAPFMHKKNARLVTPGNIEDDLPQLADCDWIIEAIVERLAIKQDLYRKLA 107

Query: 124 EHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDI 183
             RK  +I+SSNTS I + E+  G  DDF AHF+ THFFNP RY++LLEI+  ++TD D 
Sbjct: 108 AVRKADAIISSNTSSIPLHELVAGLPDDFAAHFMITHFFNPPRYMRLLEIVTSEQTDQDA 167

Query: 184 LKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLI 243
           ++ ++ F +  LGKGVV  KDTP FIANRIG + +   +QE +  G  V E D++ G  +
Sbjct: 168 VEKISQFCDFKLGKGVVPCKDTPGFIANRIGIFWIQTAIQEAIDMGLTVEEADAVVGRPM 227

Query: 244 GRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGSKAG 301
           G PK+  F   D+VG+D   H+ R++      D+  +E   IP  + +M++ G+ G K  
Sbjct: 228 GIPKTGVFGLSDLVGIDLMPHLMRSMNRSLPTDDPLREKATIPPLIQNMIDTGYTGRKGK 287

Query: 302 QGFYK--KEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRL 359
            GFY+  ++G      + + L  GE    +   L++ K  +     ++ALI   D+ G+ 
Sbjct: 288 GGFYRLNRDGGQ-KSKESIDLQTGEYNPSQPAKLDSVKATR--DGGLQALIAHPDKGGQY 344

Query: 360 LWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLG 419
            W + SQTL Y+A L+ EIADDI A++ AMK G+ W+ GPFE+ D +G    A++LE  G
Sbjct: 345 AWRVLSQTLRYAAALVPEIADDICAVNTAMKLGYNWKFGPFELIDQLGADDFAQRLEADG 404

Query: 420 ADMPGWIKEMLDKGNETFY-IKENGTVFYYDRGEYRAVKENKKRIHLQALKETKGVIAKN 478
            D+P  +    + G   FY   EN T++    G Y  ++     + L  LK     + +N
Sbjct: 405 QDVPPLLTMAREHG---FYRHNENETLYLQPDGSYLPLQRPPGVLLLADLKRHAEPLLEN 461

Query: 479 SGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGAN 538
             ASL D+GD VA LEFHSK N++   I++MI + +E    ++K LVI N+G NF  GAN
Sbjct: 462 DAASLWDIGDGVACLEFHSKMNSLDPLILEMIEETVELIPHHHKALVIYNEGSNFSAGAN 521

Query: 539 LAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARIQ 598
           L +++   +   + EVD ++   Q+    +KY+  PV+ APFGM LGGG E  L    +Q
Sbjct: 522 LGLLMFAAKLGGWDEVDKMVSGGQQAYKTLKYAPFPVIGAPFGMALGGGCEILLHCDALQ 581

Query: 599 AASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKVSASA 655
           A +E Y+GLVE+GVGLIPG GG KE+   +  + R    P+   +K FE I++A V+ SA
Sbjct: 582 AHAETYVGLVETGVGLIPGWGGCKEMLHRWSTNPRMPRGPLPPVLKCFEIISVATVAKSA 641

Query: 656 QEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLLG 715
            EA++   L+ TD I++N+D LL DAK  A S+ + G++PP      +PG T   A+ + 
Sbjct: 642 FEAKDYLFLRHTDGITMNRDRLLADAKARALSMVE-GYQPPEPPVFHLPGATARVAMEMA 700

Query: 716 AEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQA 775
               +  G  + +D  +A+ LA V++GG       + E+ LL +E   F  L  + ++ A
Sbjct: 701 VNDFRTQGKATPYDAVVAQALASVLSGGDTDMTDTLSEDDLLALEYAQFTQLVRKPETLA 760

Query: 776 RMQHMLVKGKPLRN 789
           R+ HML  GKPLRN
Sbjct: 761 RVGHMLETGKPLRN 774


Lambda     K      H
   0.316    0.134    0.382 

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: 1420
Number of extensions: 61
Number of successful extensions: 6
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: 789
Length of database: 774
Length adjustment: 41
Effective length of query: 748
Effective length of database: 733
Effective search space:   548284
Effective search space used:   548284
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)

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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