GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Coprobacter fastidiosus NSB1

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_022603146.1 NSB1T_RS28555 AMP-binding protein

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_000473955.1:WP_022603146.1
          Length = 550

 Score =  144 bits (362), Expect = 1e-38
 Identities = 136/558 (24%), Positives = 233/558 (41%), Gaps = 50/558 (8%)

Query: 27  FLDRAAVVHPTRKSVIHGSRE--YTWRQTYDRCRRLASALADRSIGPGSTVAIIAPNIPA 84
           FL+  A   P ++ +++  R+  +T+ +   R   LA  +    +   S V I A N+P 
Sbjct: 11  FLEYWAEKTPDKEFIVYSDRDLRFTYSEFNKRVNNLAKGMMAIGVEKDSKVGIWATNVPD 70

Query: 85  MYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMV-----DQEFFTLAEDSLRL 139
                F     GA+L  VN       + +L+ ++    + +     D ++  +    L  
Sbjct: 71  WLTFLFASAKIGAILVTVNTNYKQHELEYLVENADIHTLCISNGTFDSDYVDMTYTMLPE 130

Query: 140 MEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADE--- 196
           ++       K      + +     +  +R +   A    + L  G+     +    +   
Sbjct: 131 LKTSQRGHLKSNKFPYMRNVVYIGQEKHRGMYNTA----ELLLLGNTITDEKLETQKQKF 186

Query: 197 --WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWC 254
             +  + + YTSGTT  PKGV+L H                 +       +P+FHC G  
Sbjct: 187 NCYDVVNMQYTSGTTGFPKGVMLTHHNITNNGYCIGQCMKFSENDRVCLPVPLFHCFGIV 246

Query: 255 FP-WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPH 313
               ++    G ++ L +     V + + K + T     P +  A +N P   ++  L  
Sbjct: 247 LGIMAIITNGGCAVMLERFDPLVVLASVHKERCTALYGVPTMFIAELNHPMF-SMFDLSS 305

Query: 314 TVHVMTAGAAPPPSVLFSMNQKGF--RVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371
               + AG+  P  ++  +  K +   +   YGL+ET                P  TQ+K
Sbjct: 306 LRTGIMAGSLCPEWLMREVMDKMYMKEITSVYGLTETS---------------PGMTQSK 350

Query: 372 LNARQGVRYTGME------QLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEAN 425
           ++    VR + +       ++ VID +T +  P      GE+  RG  +MKGY K PEA 
Sbjct: 351 VDDPVEVRASTVGSDLPGVEVRVIDPETLEECPVG--VQGEMCCRGYNIMKGYYKMPEAT 408

Query: 426 KETF-AGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEAS 484
                  G+ HSGD+ +K P+   +I  R KD+II GGENI   E+E  +Y  P + +  
Sbjct: 409 AAIIDKNGFLHSGDLGIKTPEGNYKITGRIKDMIIRGGENIYPREIEEFLYQIPQIKDVQ 468

Query: 485 VVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVF-GPLPK 543
           V A P +++ E   AF+ LK     HD      D+  FC+ K+  + +PK + F    P 
Sbjct: 469 VAAVPSKKYGEEVGAFIILKEGESLHD-----CDVKDFCKGKISRHKIPKYIFFIDQFPL 523

Query: 544 TATGKIQKHILRTKAKEM 561
           T +GKIQK+ L+    E+
Sbjct: 524 TGSGKIQKYKLKDLGLEL 541


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: 647
Number of extensions: 28
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 569
Length of database: 550
Length adjustment: 36
Effective length of query: 533
Effective length of database: 514
Effective search space:   273962
Effective search space used:   273962
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