GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Algoriphagus aquaeductus T4

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_111391465.1 CLV31_RS03385 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_003253485.1:WP_111391465.1
          Length = 801

 Score =  718 bits (1854), Expect = 0.0
 Identities = 384/801 (47%), Positives = 524/801 (65%), Gaps = 12/801 (1%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M++ I+K AVLGSGVMGS IA H ANIG+ VLLLDIVP +LT+EE+KKGLTKD   VR+R
Sbjct: 1   MNRTIKKVAVLGSGVMGSRIACHFANIGVQVLLLDIVPFELTEEEQKKGLTKDHPAVRNR 60

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

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            V+++RK G++++SNTSGI +  M EGRS+DF+ HF GTHFFNP RYL+LLEIIP  +T 
Sbjct: 121 KVEKYRKPGTLITSNTSGIPMHLMCEGRSEDFQTHFAGTHFFNPPRYLRLLEIIPGPKTK 180

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
           P+I+ F+  +G+  LGK  V  KDTP FIANRIG Y ++  +  + K G+ V EVD +TG
Sbjct: 181 PEIIDFLMDYGDRYLGKETVLCKDTPAFIANRIGVYAIISGMHAIEKAGFGVSEVDKLTG 240

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299
           P+IGR KSATFRT+DVVGLDT  +VA N++     DE ++ F++P  +  +    W G K
Sbjct: 241 PVIGRAKSATFRTMDVVGLDTTVNVANNLHKALPHDESRDKFKLPKIVEVLYNNKWFGDK 300

Query: 300 AGQGFYK----KEG-KTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354
            GQG++K    K+G K + ELD  T  Y +  K K  ALEA+K+    K ++K L+  DD
Sbjct: 301 TGQGYFKMIRHKDGSKELKELDLKTFEYKDVEKPKFKALEASKEIDDLKKRIKFLVNFDD 360

Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414
           RAG            Y +  + EI+D+++ IDQA+  GFGWELGPFE WD +G+K++ EK
Sbjct: 361 RAGEFYRASFYDLFKYCSHRIPEISDELYRIDQAVCAGFGWELGPFETWDVLGVKETVEK 420

Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472
           +E  G     W+ EML  G+++FY  ENG   YYD     Y  +   +  I L  LK   
Sbjct: 421 MEAAGEKAAPWVHEMLGAGHDSFYKVENGKRKYYDIPSKSYVEIPGIEDFIILDTLKSAG 480

Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532
             +  N+G+++ D+GD+V  LEFH+K N++G ++I+ I+  +   E++YKGLVIGN+G N
Sbjct: 481 KKVWGNAGSTIYDMGDEVIGLEFHTKMNSMGAEVIEGINTAIGMAEKSYKGLVIGNEGGN 540

Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592
           F  GANLAM+ M   D  F E++ +I +FQ TMM+ +YS+ PVV AP  M LGGG E  L
Sbjct: 541 FSAGANLAMLFMFAGDQEFDEINLMIAQFQNTMMRARYSSVPVVVAPHNMALGGGCELSL 600

Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMA 649
            A  IQA +E YMGLVE GVGLIP GGG KE+   + N +  G   +N   + F  IA A
Sbjct: 601 HADHIQAHAELYMGLVEVGVGLIPAGGGTKEMTRRFANGVIAGDVELNQLQEYFMNIATA 660

Query: 650 KVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKE-KVKVPGETG 708
           KVS SA+EAR +  L+  D IS+N+   L DAK    SL D G+  P ++  +KV G+T 
Sbjct: 661 KVSTSAEEARGLGYLRTQDGISLNRKRQLADAKAKVLSLSDLGYTQPAQQTNIKVLGKTS 720

Query: 709 YAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLS 768
            A    G   M    YISEHD KIA+KLA+V++GG +   TEV E+YLL++EREAFLSL+
Sbjct: 721 LALFEAGITGMIYGNYISEHDAKIARKLAWVMSGGDLSSPTEVSEQYLLDLEREAFLSLT 780

Query: 769 GEAKSQARMQHMLVKGKPLRN 789
           GE K+  R+  +L KGKPLRN
Sbjct: 781 GEQKTLERIHSILFKGKPLRN 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: 1523
Number of extensions: 73
Number of successful extensions: 8
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 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