GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_1069
          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:

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