GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Herbaspirillum seropedicae SmR1

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate HSERO_RS00095 HSERO_RS00095 AMP-dependent synthetase

Query= SwissProt::Q8GQN9
         (527 letters)



>FitnessBrowser__HerbieS:HSERO_RS00095
          Length = 539

 Score =  204 bits (518), Expect = 9e-57
 Identities = 166/530 (31%), Positives = 252/530 (47%), Gaps = 22/530 (4%)

Query: 12  TPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAG----SYTYDELALRVNRCGSALR 67
           +P   +IP  +N A     R    G G   +  +DA     SY+YD+L +  +R  +ALR
Sbjct: 12  SPYEWQIPTHFNIAQAACDR-WADGSGRTAIICEDADGSVTSYSYDQLKILSDRFANALR 70

Query: 68  TTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAV 127
              G+   DR+ + +   I+   T L A K G + + +  L       Y L +S A VA+
Sbjct: 71  AA-GVGRGDRIGIYLSQRIETVITHLAAYKLGAITVPLFYLFGPDAIAYRLDNSGA-VAL 128

Query: 128 VSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAP-------TRPDD 180
           V+       A + G++P L   +V      D +        ++  AAP       T  DD
Sbjct: 129 VTDASGMEKATLAGELPALR--LVFCVESSDLVLPQTTDFWDRLHAAPAELDPVLTLADD 186

Query: 181 HCFWLYSSGSTGAPKGTVHIHSDLI-HTAELYARPILGIREGDVVFSAAKLFFAYGLGNG 239
               +Y+SG+TG  KG +H H  L+ H   +        +EGD  ++ A   +  GL + 
Sbjct: 187 PAMIIYTSGTTGKAKGALHAHRVLLGHLPGVEVSHDSFPQEGDRFWTPADWAWIGGLLDV 246

Query: 240 LIFPLAVGATAVLMA-ERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRL 298
           L+  L  G   V    E+   A VF  L RHQ    +  PT    +        + +  L
Sbjct: 247 LLPSLYHGVAVVARRLEKFDAAEVFGLLARHQIRNVFFPPTALKMLRGAATVRAQADFSL 306

Query: 299 RACTSAGEALPEDVGRRWQARFGVDILDGIGSTEM-LHIFLSNRAGDVHYGTSGKPVPGY 357
           R+  S GE L +D+    +   GV I +  G TE  L +  S+       G+ G+ VPG+
Sbjct: 307 RSVASGGETLGDDLIAWGREALGVTINEFYGQTECNLVVSSSSHCYPSVSGSMGRAVPGH 366

Query: 358 RLRLIDEDGAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVND 415
            ++++DE G ++   G  G + I  P   +   YW N E T   F G++  +GD   +++
Sbjct: 367 VVQIVDEQG-QVLPHGTVGNIAIRAPDPVMFLRYWRNEEATREKFAGDFLLTGDLGSMDE 425

Query: 416 EGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLK 475
           +GY  Y GR+DD++  +G  + P  +E  L+ H AV  AAVVG +D       KAF+VLK
Sbjct: 426 QGYIRYLGRNDDVITSAGYRIGPAAIEECLMRHPAVRIAAVVGVKDALRTEVVKAFVVLK 485

Query: 476 PGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
            G    EAL+ +L+ HV+  LA ++YPR I FV  LP TATGKI R  L+
Sbjct: 486 DGVTPDEALKAELQQHVRAQLAAHEYPRLISFVAALPTTATGKIMRKTLK 535


Lambda     K      H
   0.319    0.138    0.412 

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: 732
Number of extensions: 27
Number of successful extensions: 5
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: 527
Length of database: 539
Length adjustment: 35
Effective length of query: 492
Effective length of database: 504
Effective search space:   247968
Effective search space used:   247968
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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