Aligments for a candidate for acs in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Herbaspirillum seropedicae SmR1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate HSERO_RS00095 HSERO_RS00095 AMP-dependent synthetase

Query= curated2:O93730
         (670 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS00095 HSERO_RS00095
           AMP-dependent synthetase
          Length = 539

 Score =  226 bits (576), Expect = 2e-63
 Identities = 185/575 (32%), Positives = 270/575 (46%), Gaps = 55/575 (9%)

Query: 67  ASNPPFYKWFVGGRLNLSYLAVDRHVKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDL 126
           A NP  Y+W +    N++  A DR        + AI  E        Y  D+ K+   D 
Sbjct: 8   AGNPSPYEWQIPTHFNIAQAACDRWADG--SGRTAIICEDADGSVTSYSYDQLKILS-DR 64

Query: 127 YREVNRVAYMLKQNFGVKKGDKITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALA 186
           +    R A       GV +GD+I +YL    E  IT LAA+++GAIT  +F  F  DA+A
Sbjct: 65  FANALRAA-------GVGRGDRIGIYLSQRIETVITHLAAYKLGAITVPLFYLFGPDAIA 117

Query: 187 ERINDSQSRIVITADGFWRRGRVVRLKEVVDAA-LEKATGVESVIVLPRLGL------KD 239
            R+++S +  ++T                 DA+ +EKAT       LP L L       D
Sbjct: 118 YRLDNSGAVALVT-----------------DASGMEKATLAGE---LPALRLVFCVESSD 157

Query: 240 VPMTEGRDYWWNKLMQGIPPNAYIEPEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVH 299
           + + +  D+W    +   P  A ++P    ++ P+ I+YTSGTTGK KG +H       H
Sbjct: 158 LVLPQTTDFW--DRLHAAP--AELDPVLTLADDPAMIIYTSGTTGKAKGALHAHRVLLGH 213

Query: 300 VYAT-MKWVFDIRDDDIFWCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWW 358
           +    +      ++ D FW  AD  W+ G   V+L P L     V+      +   + + 
Sbjct: 214 LPGVEVSHDSFPQEGDRFWTPADWAWIGGLLDVLL-PSLYHGVAVVARRLEKFDAAEVF- 271

Query: 359 SIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHDLSTLRIIHSVGEPINPEAWRWAYRVLG 418
            ++ R+ +   +  PTA++M    G    R     +LR + S GE +  +   W    LG
Sbjct: 272 GLLARHQIRNVFFPPTALKMLR--GAATVRAQADFSLRSVASGGETLGDDLIAWGREALG 329

Query: 419 NEKVAFGSTWWMTETGGIVISHAPGLYLVPMKPGTNGPPLPGFEVDVVDENGNPAPPGVK 478
              V     +  TE   +V S +   +  P   G+ G  +PG  V +VDE G   P G  
Sbjct: 330 ---VTINEFYGQTECNLVVSSSS---HCYPSVSGSMGRAVPGHVVQIVDEQGQVLPHGTV 383

Query: 479 GYLVIKKPWPGMLHGIWGDPERYIKTYWSRFPGMFYAGDYAIKDKDGYIWVLGRADEVIK 538
           G + I+ P P M    W + E   + +   F      GD    D+ GYI  LGR D+VI 
Sbjct: 384 GNIAIRAPDPVMFLRYWRNEEATREKFAGDF---LLTGDLGSMDEQGYIRYLGRNDDVIT 440

Query: 539 VAGHRLGTYELESALISHPAVAESAVVGVPDAIKGEVPIAFVVLKQGVAPSDELRKELRE 598
            AG+R+G   +E  L+ HPAV  +AVVGV DA++ EV  AFVVLK GV P + L+ EL++
Sbjct: 441 SAGYRIGPAAIEECLMRHPAVRIAAVVGVKDALRTEVVKAFVVLKDGVTPDEALKAELQQ 500

Query: 599 HVRRTIGPIAEPAQIFFVTKLPKTRSGKIMRRLLK 633
           HVR  +     P  I FV  LP T +GKIMR+ LK
Sbjct: 501 HVRAQLAAHEYPRLISFVAALPTTATGKIMRKTLK 535


Lambda     K      H
   0.319    0.138    0.440 

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: 905
Number of extensions: 43
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: 670
Length of database: 539
Length adjustment: 37
Effective length of query: 633
Effective length of database: 502
Effective search space:   317766
Effective search space used:   317766
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources