GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Microvirga lotononidis WSM3557

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate WP_009763961.1 MICLODRAFT_RS21665 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_000262405.1:WP_009763961.1
          Length = 546

 Score =  615 bits (1586), Expect = e-180
 Identities = 304/549 (55%), Positives = 384/549 (69%), Gaps = 17/549 (3%)

Query: 11  DLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIG 70
           +L K PANY  LTPL FL+RAA VHP R +VIHG     +R  Y R RRLASALA R IG
Sbjct: 9   NLDKNPANYQPLTPLSFLERAASVHPDRTAVIHGPLVRDYRDFYARARRLASALARRGIG 68

Query: 71  PGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFF 130
            G TV+++ PN PAM E H+GVPM GAVLN +N RL+A  +AF L HS++ V++ D+EF 
Sbjct: 69  RGDTVSVMLPNTPAMLECHYGVPMAGAVLNTLNTRLDAKIIAFSLDHSEAKVLITDREFS 128

Query: 131 TLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPW 190
              + +L      A SS K PL+I   D    PE        GA+EYE+FLA GDP + W
Sbjct: 129 ATVKAAL------ARSSVK-PLVIDYDD----PEFTGPGERLGAMEYEEFLAEGDPEFAW 177

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
            PP DEW +I L YTSGTT  PKGVV HHRGAY++A+ N L  GM    VYLWTLPMFHC
Sbjct: 178 NPPRDEWDAITLNYTSGTTGDPKGVVYHHRGAYLLAMGNILTAGMGQHPVYLWTLPMFHC 237

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWCFPWSL++++G  +CLR V AK +Y  +A  +VTH C AP+V++ ++NAP  +   P
Sbjct: 238 NGWCFPWSLSIVAGIHVCLRAVRAKPMYDALADQRVTHLCGAPIVMSTLLNAPASEK-RP 296

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
           LPHTV  +TA A PP +VL +M   GF V H YGL+E YGP+ V  W  EWD+L     A
Sbjct: 297 LPHTVKFLTAAAPPPEAVLAAMKAAGFDVTHLYGLTEVYGPAVVNEWHDEWDALDQGGYA 356

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
              ARQGVRY  +E LDV+D +T +PVPADG+T GE++FRGN+VMKGYLKNP    + F 
Sbjct: 357 AKKARQGVRYPVLEALDVLDPETMQPVPADGRTLGEVMFRGNVVMKGYLKNPSGTAKAFE 416

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GGWFHSGD+ VK+PD Y+++KDRSKD+IISGGENISS+EVE+ +Y HPA+  A+VVA PD
Sbjct: 417 GGWFHSGDLGVKYPDGYVQLKDRSKDIIISGGENISSIEVEDALYRHPAIQAAAVVAMPD 476

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
           E+W E+PCAFV L+      DQ+  A+DI+ +CR+ L +Y  P++V+F  LPKT+TGKIQ
Sbjct: 477 EKWGETPCAFVELRP-----DQSVPAEDIIAWCRQHLASYKCPRTVIFTELPKTSTGKIQ 531

Query: 551 KHILRTKAK 559
           K  LR  A+
Sbjct: 532 KFQLREMAR 540


Lambda     K      H
   0.319    0.134    0.422 

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: 933
Number of extensions: 35
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: 569
Length of database: 546
Length adjustment: 36
Effective length of query: 533
Effective length of database: 510
Effective search space:   271830
Effective search space used:   271830
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 (21.8 bits)
S2: 53 (25.0 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