GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Flavobacterium glycines Gm-149

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_066324596.1 BLR17_RS15685 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_900100165.1:WP_066324596.1
          Length = 796

 Score =  718 bits (1853), Expect = 0.0
 Identities = 384/797 (48%), Positives = 516/797 (64%), Gaps = 9/797 (1%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + I+K AV+GSG+MGSGIA H ANIG+ VLLLDI+P +LT+ E KKGLT +S  VR+R
Sbjct: 1   MKRTIKKVAVIGSGIMGSGIACHFANIGVEVLLLDIIPKELTETESKKGLTLESKVVRNR 60

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           +  + +   LK KP+P+ SAK  S I+  N  DD  K+   DWIIEVVVE L+VKK +F 
Sbjct: 61  IVNEHLANSLKSKPSPIYSAKFASRISTRNTTDDMAKIAAVDWIIEVVVERLDVKKLVFE 120

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            +D++R  G++V+SNTSGI +  M+EGRS+DF+ HF GTHFFNPARYLKL EIIP  +T 
Sbjct: 121 QIDKYRTPGTLVTSNTSGIPIHFMSEGRSEDFQKHFCGTHFFNPARYLKLFEIIPGPKTS 180

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
            ++L F+  +GE  LGK  V AKDTP FI NRIG +G+      + + G  + +VD +TG
Sbjct: 181 SEVLDFLKNYGEQFLGKTSVVAKDTPAFIGNRIGVFGIQSLFHLVKEMGLTIEQVDKLTG 240

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299
           P+IGRPKSATFRT+DVVGLDT  HVA  +Y+    DE  E+F++P F+  M+E  W GSK
Sbjct: 241 PVIGRPKSATFRTVDVVGLDTLVHVANGIYENCPEDEAHELFQLPEFIKKMVENKWFGSK 300

Query: 300 AGQGFYKKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRL 359
            GQGFYKK  K I  LD  TL Y    K     LE  K  +    + K LI   D+AG  
Sbjct: 301 TGQGFYKKVDKDILSLDLDTLEYRPAKKTSFATLELTKTIEKPIDRFKVLIKGQDKAGEF 360

Query: 360 LWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLG 419
                +    Y +  + EI+D+++ ID AMK GFGWE GPFE+WDAIG+++  E ++  G
Sbjct: 361 YRKSFAALFAYVSNRIPEISDELYKIDNAMKAGFGWENGPFEIWDAIGVEKGIEMIKAEG 420

Query: 420 ADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETKGVIAK 477
                W+ EML  G+ +FY  + G  ++YD  +     V      I L  ++E+K V + 
Sbjct: 421 YTPAPWVNEMLASGSSSFYTIKEGATYFYDISKKSQEKVPGQDAFIILNNIRESKKVWS- 479

Query: 478 NSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGA 537
           NSGA + DLGD +  +EF SK N IG D++Q I+KG++  E+ Y GLVIGNQ  NF VGA
Sbjct: 480 NSGAIIEDLGDGILNIEFKSKMNTIGGDVLQAINKGIDLAEKEYSGLVIGNQAANFSVGA 539

Query: 538 NLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARI 597
           N+ MI M   +  + E++  I+ FQ+TMM+++YS+ PVV AP GMT GGG E  L A ++
Sbjct: 540 NIGMIFMMAVEQEYDELNMAIKLFQDTMMRVRYSSIPVVVAPHGMTFGGGCEMSLHADKV 599

Query: 598 QAASEAYMGLVESGVGLIPGGGGNKELYI---NHLRRGHDPMNAAMKTFETIAMAKVSAS 654
            AA+E YMGLVE GVG+IPGGGG+KE+ +   +  R+    +N   + F TIAMAKVS S
Sbjct: 600 VAAAETYMGLVEFGVGVIPGGGGSKEMTLRAADLFRKNDVELNTLQEYFLTIAMAKVSTS 659

Query: 655 AQEAREMNILKE-TDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEK-VKVPGETGYAAL 712
             EA +  +L+   D I VN+D  + +AK+ A  + + G+  P++   +KV G+      
Sbjct: 660 GYEAFDTGLLQHGKDIIVVNKDRQIAEAKKHALLMAEAGYTQPIRRNDIKVLGKQALGMF 719

Query: 713 LLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAK 772
           L+G +QM    YISEHD KIA KLAYV+AGG +   T V E+YLL++EREAFLSL  E K
Sbjct: 720 LVGTDQMVAGSYISEHDKKIANKLAYVMAGGDLSEPTLVSEQYLLDLEREAFLSLCTERK 779

Query: 773 SQARMQHMLVKGKPLRN 789
           +  R+Q+ML  GKPLRN
Sbjct: 780 TLERIQYMLKAGKPLRN 796


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: 1467
Number of extensions: 62
Number of successful extensions: 7
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: 796
Length adjustment: 41
Effective length of query: 748
Effective length of database: 755
Effective search space:   564740
Effective search space used:   564740
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