Alignments for a candidate for fadB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Pedobacter sp. GW460-11-11-14-LB5

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate CA265_RS17590 CA265_RS17590 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>FitnessBrowser__Pedo557:CA265_RS17590
          Length = 802

 Score =  731 bits (1888), Expect = 0.0
 Identities = 392/802 (48%), Positives = 521/802 (64%), Gaps = 14/802 (1%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + I K AVLGSG+MGS IA H ANIG+ VLLLDI P +L+ EE+ KGLT D+  V++R
Sbjct: 2   MKRSINKVAVLGSGIMGSRIACHFANIGVEVLLLDIAPKELSPEEQAKGLTLDNPAVKNR 61

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           +   A++  +K  P+P+ + K  + I  GN  DD  K+   DW+IEVVVENL++KKK+F 
Sbjct: 62  IVNTALQTAVKTNPSPVYTKKALNKIKTGNFADDMSKIAGYDWVIEVVVENLDIKKKVFE 121

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            V++ RK G++++SNTSGI +  MAEGRS+DFKAHF GTHFFNP RYLKLLEIIP   T 
Sbjct: 122 QVEQFRKPGTLITSNTSGIPIHLMAEGRSEDFKAHFCGTHFFNPPRYLKLLEIIPTPHTQ 181

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
           P+I+ F+  +G+  LGK  V  KDTP FIANR+G Y ++  +  + K    V EVD  TG
Sbjct: 182 PEIVDFLMHYGDKFLGKTTVLCKDTPAFIANRVGVYSIMALLHLVEKLDLTVEEVDKFTG 241

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299
           P +GRPKSATFRT DVVGLDT   VA+ +YD    D+  ++F++P+++  M E  W+G K
Sbjct: 242 PALGRPKSATFRTSDVVGLDTMIKVAKGLYDNCPDDKAHDLFKLPAYVQKMEENKWLGDK 301

Query: 300 AGQGFYKK----EGKT-IYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354
             QGFYKK    +GKT I  LD  TL Y  + K+KS  LE  K  +  + +MK      D
Sbjct: 302 TQQGFYKKTKSADGKTEILALDLKTLEYKPQQKVKSATLEMTKPIENLRERMKIFAKGKD 361

Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414
           +AG L  + +     Y ++ + EI+D+++ ID AM+ GFGWELGPFE+WDA+G+K++ E 
Sbjct: 362 KAGELFRHSSFGLFEYVSDRIPEISDELYRIDDAMRAGFGWELGPFELWDAVGVKEAIEG 421

Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472
           +EQ G     W+ EMLD GN +FY  ENG   YYD     Y+A+    + I L  L+E K
Sbjct: 422 MEQYGNKAAAWVHEMLDAGNTSFYKVENGVKKYYDIPSKSYKALPGTDEFIILDNLRENK 481

Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532
             + KNSG S+IDLGD +  +EFH+K N IG D+I  I+K ++  E++Y+GLVIGN G N
Sbjct: 482 -TLWKNSGVSIIDLGDGILNVEFHTKMNTIGGDVISGINKAIDMAEKDYRGLVIGNDGAN 540

Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592
           F  GAN+ MI M   +  + E++  IR FQ T M+I+YS+ PVV AP  +TLGGG E  L
Sbjct: 541 FSAGANVGMIFMMAVEQEWDELNMAIRMFQNTSMRIRYSSIPVVVAPHNLTLGGGCEFSL 600

Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKELYINHLRRGHDP---MNAAMKTFETIAMA 649
            A  +Q ++E YMGLVE GVG+IPGGGG KE  +       D     NA    F TI MA
Sbjct: 601 HADHVQLSAETYMGLVEFGVGVIPGGGGTKEFALRASDEYKDDQIVQNALKDRFLTIGMA 660

Query: 650 KVSASAQEAREMNIL-KETDQISVNQDHLLYDAKQLAASLYDTGWRPPV-KEKVKVPGET 707
           KVS S  EA E+  L K+   IS+N++ LL DAK  A  L D G+  PV +  +KV G+ 
Sbjct: 661 KVSTSGYEAYELGYLQKDKFSISMNRNRLLADAKAKAIELADAGYTKPVQRNDIKVLGKQ 720

Query: 708 GYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSL 767
           G   +  GA  M    +ISEHD KI++KL YV+ GG +   TEV E+YLL++EREAFLSL
Sbjct: 721 GLGIVYAGANSMYAGHFISEHDKKISEKLGYVMCGGDLSAPTEVTEQYLLDLEREAFLSL 780

Query: 768 SGEAKSQARMQHMLVKGKPLRN 789
           +GE KS  R+Q ++ KGKPLRN
Sbjct: 781 AGERKSLERIQSIITKGKPLRN 802


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: 1492
Number of extensions: 76
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: 802
Length adjustment: 41
Effective length of query: 748
Effective length of database: 761
Effective search space:   569228
Effective search space used:   569228
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources