GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Erythrobacter gangjinensis K7-2

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_047005493.1 AAW01_RS00825 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_001010925.1:WP_047005493.1
          Length = 776

 Score =  541 bits (1395), Expect = e-158
 Identities = 308/797 (38%), Positives = 463/797 (58%), Gaps = 34/797 (4%)

Query: 3   KHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLS 62
           K I+K  V+G+G MG+GIAA +AN G+PVLLLDI+P +               + R+ ++
Sbjct: 4   KSIKKVCVIGAGTMGAGIAAQIANAGVPVLLLDILPKE--------------GDNRNAVA 49

Query: 63  RQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALV 122
             A+ K+LK +PAP    +    +  GN+EDD  K+ E DW++E ++E L++K+ ++A +
Sbjct: 50  EGAVAKMLKTQPAPFMGKRAAKLVETGNIEDDLGKVAECDWVVEAIIERLDIKQDLYAKL 109

Query: 123 DEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPD 182
           +E R  G+ VSSNTS I + ++ +GRSD FK  FL THFFNP RY++L+EI+   +++ D
Sbjct: 110 EEVRTPGTAVSSNTSTIPLAQLTDGRSDQFKQDFLITHFFNPPRYMRLIEIVAGPQSNAD 169

Query: 183 ILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPL 242
            +  ++ F +  LGK VV A+D+P FIANR+GT+ +   V      G  V E D I G  
Sbjct: 170 TVDMVSDFVDRKLGKTVVDAEDSPGFIANRVGTFWIQQAVNSAFDLGITVEEADEIGGRP 229

Query: 243 IGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGSKA 300
           +G PK+  F  +D++G+D   H+ +++      D+  +++ R    +  M++ G+ G K 
Sbjct: 230 MGVPKTGLFGLIDLIGIDLMPHLMKSLTSTLPADDWYQKIARSEPLIEAMIKDGYTGRKG 289

Query: 301 GQGFYKKE----GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRA 356
             GFY+      GK     D   L  GE      P L     AKG    +KALI +  + 
Sbjct: 290 LGGFYRINRDGGGKVKEAKD---LKSGEYRAAARPGLVRGPAAKG---DLKALISAKGKV 343

Query: 357 GRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLE 416
           G   W +   TL Y+A ++ E    I  +D AMK G+ W+ GPFEM DAIG     E+L+
Sbjct: 344 GDYAWAVLGPTLSYAASIVPEATATIVGVDDAMKLGYNWKRGPFEMIDAIGAAHLVERLK 403

Query: 417 QLGADMPGWIKEMLDKGNETFYIKENGTVFYYDR-GEYRAVKENKKRIHLQALKETKGVI 475
           +    +P  ++++   G+ TFY  ++G   Y+   GEY  V   +  + L+ +K T   +
Sbjct: 404 ESDYPVPAILEQI---GDRTFYRVQDGKRQYFGTDGEYHDVVRPEGVLLLEDIKLTGEPL 460

Query: 476 AKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCV 535
            KN  A+L DLGD V  LEF  K NA+   ++++I K +   +++YK LV+ N+G NF  
Sbjct: 461 IKNGSAALWDLGDGVVALEFTGKMNALDEQVMRLIQKAIPLVKKDYKALVVYNEGSNFSA 520

Query: 536 GANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAA 595
           GANL + L  +    + EV+  ++  Q     +KY+  PVV+APFG+ LGGG E CL + 
Sbjct: 521 GANLGLALFALNIAAWGEVEKSVKGGQAAYKALKYAPFPVVSAPFGLALGGGCEVCLNSD 580

Query: 596 RIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKVS 652
            IQA +E Y+GLVE+GVG+IPG GG  E+   +  + R  + PM A  K+FE I+ A V+
Sbjct: 581 AIQAHAETYIGLVETGVGIIPGWGGCGEMISRWEENPRHPNGPMPAVSKSFELISTATVA 640

Query: 653 ASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAAL 712
            SA EA++   L+  D I++N+D LLYDAKQ A ++ D G+  P K + ++PG TG AAL
Sbjct: 641 KSAAEAKDHGFLRRDDGITMNRDRLLYDAKQRALAMVD-GYEAPEKPEYRLPGPTGAAAL 699

Query: 713 LLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAK 772
            L  +  +  G  +EHD  +A +LAYV+ GG       V E+ +L+ E EAF+ L    K
Sbjct: 700 KLAVDSFRKQGLATEHDETVAHELAYVLTGGDTDMIDVVTEDQMLKFEAEAFMRLVRNPK 759

Query: 773 SQARMQHMLVKGKPLRN 789
           SQAR++HML  GKPLRN
Sbjct: 760 SQARVEHMLETGKPLRN 776


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: 1473
Number of extensions: 84
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: 776
Length adjustment: 41
Effective length of query: 748
Effective length of database: 735
Effective search space:   549780
Effective search space used:   549780
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 Sep 24 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