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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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