GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Bacillus altitudinis 41KF2b

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_035703058.1 BA79_RS12435 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_000691145.1:WP_035703058.1
          Length = 502

 Score =  209 bits (533), Expect = 2e-58
 Identities = 152/492 (30%), Positives = 229/492 (46%), Gaps = 25/492 (5%)

Query: 48  YTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLS 107
           YT+  +   +   A  L R+G  + D++ FI +N   F         AG V VP++++L+
Sbjct: 28  YTFEEYAKRIDQLAHYLHRKGIRKGDRVCFICQNHHHFSTIMLAAIKAGAVAVPLSWQLT 87

Query: 108 PKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTY 167
             E+  I+  ++ K +  D        E +D I A  + LED     +   A+      +
Sbjct: 88  SFELEGILKKAEPKALFFDR-------EFRDIIAAVNVSLEDCLMVESGVNAK--TTQLF 138

Query: 168 RELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDL 227
            +++       L     EE  +  + +TSGTTG PKG M  H G     +        DL
Sbjct: 139 EDILASNDGSDLAEQVSEE-DLAMILFTSGTTGNPKGCMVGH-GRIYQFLTRRGNRGFDL 196

Query: 228 NSV-YLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVY 286
               YL + P++H +S     A    G T V L       I   +EKER+T M A P+ Y
Sbjct: 197 KGKRYLASHPLYHMSSINHLIAAAIEGYTLVFLHDATPKRILETIEKERITFMMAFPSAY 256

Query: 287 VNLADYMKRNNLKFSNRVHMLVAGAAPAPATL-KAMQEIGGYMCHVYGLTETYGPHSICE 345
             + + MKR++   S+   + ++G    P  L +  +E+G  M H YG TE +    +  
Sbjct: 257 TYMLEEMKRSSYDLSS-FEIAISGGTKVPVRLIRDYKEVGIQMMHGYGSTEAW---VVSA 312

Query: 346 WRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGY 405
           W        +    K+     +  V  E +     G+        IGEVVMR     LGY
Sbjct: 313 WHPAMGEDKMGSAGKVDPDVEVKIVHPETEEALPAGE--------IGEVVMRSPFYFLGY 364

Query: 406 YKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIP 465
           Y  PE T +  +DGWFH GDA  +  DG++ I  R+KD+I  GG+ +    VE+ + +IP
Sbjct: 365 YHQPEATEKVLKDGWFHMGDAGYLDEDGFLYITGRYKDVILYGGDNIYPDQVEEVIDQIP 424

Query: 466 GVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPM 525
           GV   AV G PD+ +GEV +A I   E V   EE+V+ +CKERLA ++ P I     +P 
Sbjct: 425 GVIESAVIGVPDDLYGEVPSAYIVKDESVDFCEEDVLNYCKERLADYKVPSIHFTHDLPK 484

Query: 526 TATGKMQKYVLR 537
              GK+ K  LR
Sbjct: 485 NKLGKIMKKDLR 496


Lambda     K      H
   0.319    0.136    0.411 

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: 659
Number of extensions: 43
Number of successful extensions: 4
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: 549
Length of database: 502
Length adjustment: 35
Effective length of query: 514
Effective length of database: 467
Effective search space:   240038
Effective search space used:   240038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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