GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate Echvi_1069 Echvi_1069 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>lcl|FitnessBrowser__Cola:Echvi_1069 Echvi_1069 3-hydroxyacyl-CoA
           dehydrogenase
          Length = 801

 Score =  709 bits (1830), Expect = 0.0
 Identities = 382/803 (47%), Positives = 521/803 (64%), Gaps = 16/803 (1%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + I+K A+LGSGVMGS IA H ANIG+ VLLLDI+P +  + E KKGL+ +   VR+R
Sbjct: 1   MKRAIQKVAILGSGVMGSRIACHFANIGVKVLLLDILPKEPNEAESKKGLSLEDKAVRNR 60

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           L  +A++K LK KP+P+        I  GN +DD  K+K+ DW+IEVVVE L++K+ ++ 
Sbjct: 61  LVNEALEKTLKSKPSPIYDRAFADRIQTGNFDDDLPKIKDYDWVIEVVVERLDIKQSLYE 120

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            V++HRK G++++SNTSGI +Q + EGRSDDF+A+F GTHFFNP RYL+LLEIIP  +TD
Sbjct: 121 KVEQHRKPGTLITSNTSGIPMQMLCEGRSDDFQANFCGTHFFNPPRYLRLLEIIPGPKTD 180

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQ--EMLKGGYQVGEVDSI 238
           P I+ F+  +G+  LGK  V  KDTP FIANRIG Y ++ ++   E +K G  V EVD +
Sbjct: 181 PAIIDFLMDYGDRHLGKETVLCKDTPAFIANRIGVYAMMSSMHIIESMKMG--VSEVDKL 238

Query: 239 TGPLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIG 297
           TG +IGR KSATFRT+DVVGLDT  +VA N+      DE K+ F++P  +  + EK W+G
Sbjct: 239 TGTVIGRAKSATFRTMDVVGLDTMVNVANNLSKALQNDESKDKFKLPKTVAYLSEKKWLG 298

Query: 298 SKAGQGFY-----KKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYS 352
            K GQGF+     K   K + E+D  T  Y    K K  ALEA+K+    K ++K L+  
Sbjct: 299 DKTGQGFFHMIRHKDGSKELKEIDLQTHEYKPAEKPKFKALEASKEINDLKERIKFLVNF 358

Query: 353 DDRAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSA 412
           DD AG            Y +  + EI+D+++ IDQA+  GFGWE GPFE WD +GLK + 
Sbjct: 359 DDEAGAFYRATFYDLFRYCSFRIPEISDELYRIDQAVCAGFGWEYGPFENWDILGLKDTI 418

Query: 413 EKLEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKE 470
           +K+E+       WI EMLD GNE FY  E+G   YYD     Y+ +   ++ I L  LK 
Sbjct: 419 KKMEEADQRPAEWIYEMLDAGNEHFYRVEDGRRQYYDIPSKSYKDIPGQQEFILLDTLKA 478

Query: 471 TKGVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQG 530
               I  N+GA++ D+GD+V  LEFH+K N++G ++I+ I+  +   E++YKGLVIGN+G
Sbjct: 479 ANKKIWGNAGATIYDMGDEVIGLEFHTKMNSLGQEVIEGINTAITMAEKDYKGLVIGNEG 538

Query: 531 KNFCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEA 590
            NF  GANLAM+ M   D  F E++ +I +FQ+TMM+++YS+ PVV AP  M LGGG E 
Sbjct: 539 ANFSAGANLAMLFMFAGDQEFDEINLMIAQFQKTMMRVRYSSVPVVVAPHNMALGGGCEM 598

Query: 591 CLPAARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIA 647
            L A  +QA +E YMGLVE GVGLIP GGG KE+   + N +  G   +N   + F  IA
Sbjct: 599 SLHADAVQAHAELYMGLVEFGVGLIPAGGGTKEMILRFSNAIHSGDVEVNRLQEYFMNIA 658

Query: 648 MAKVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKE-KVKVPGE 706
            AKVS SA+EAR +  L+  D I++N+     +AK     L+D G+  PV++  +KV G+
Sbjct: 659 TAKVSTSAEEARGLGYLQAKDDITLNRKRQFAEAKAKVIELFDEGYTQPVQQTNIKVLGK 718

Query: 707 TGYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLS 766
           T  A    G   M+   YISEHD KIA+KLA+V++GG +    EV E+YLLE+EREAFLS
Sbjct: 719 TSLALFEAGITGMRYGAYISEHDAKIARKLAWVMSGGDLSQANEVSEQYLLELEREAFLS 778

Query: 767 LSGEAKSQARMQHMLVKGKPLRN 789
           L+GE K+  R+Q +L KGKPLRN
Sbjct: 779 LTGEQKTLERIQSILFKGKPLRN 801


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: 1505
Number of extensions: 73
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: 801
Length adjustment: 41
Effective length of query: 748
Effective length of database: 760
Effective search space:   568480
Effective search space used:   568480
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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