GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS00095
          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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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