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_RS15645 HSERO_RS15645 acetyl-CoA synthetase

Query= curated2:Q9RRL7
         (649 letters)



>FitnessBrowser__HerbieS:HSERO_RS15645
          Length = 628

 Score =  505 bits (1301), Expect = e-147
 Identities = 276/628 (43%), Positives = 392/628 (62%), Gaps = 21/628 (3%)

Query: 34  EYERRYRQSLDQPDDFWSEVAHDLHWMKDWDRVLDWQEP-HAQWFVGGQTNIAYNALDRN 92
           +YE+ YRQS++QP+ FW++ A  +HW + + R LD+  P  A+WF+ GQTN+ +NA+DR+
Sbjct: 2   QYEQFYRQSVEQPEAFWAQEAQRIHWQQPFSRTLDYSRPPFARWFIDGQTNLCHNAVDRH 61

Query: 93  VQRGLGDKRAIIWEGEDGEVRTYTYAELLREVCKAANALEELGVVAGDRVTLYMPLIPEA 152
           +         I    E    R YTYAEL +EV   A +++ LGV  GDRV +YMP+I EA
Sbjct: 62  LPERAQQAALIAISTETNSERVYTYAELQQEVMAMAASMQALGVQRGDRVLIYMPMIAEA 121

Query: 153 AIAMLACARIGAVHSIVFGGFSVSALADRINNAQSKLLITADAGYRRGKPVTLKINADEA 212
             AMLACARIGAVHS+VFGGF+ ++LA RI++AQ +L+++ADAG R GK +  K   DEA
Sbjct: 122 VFAMLACARIGAVHSVVFGGFASNSLASRIDDAQPRLIVSADAGSRGGKVIPYKGLLDEA 181

Query: 213 AKLAPCL-EHVLVVKRAGIPLEWWTEGRDLWWHDV-VDRQSDQHEATALDSEHPLFILYT 270
             +A    +HVL+V R   P+   T  RD+ +  +       Q   T L+S    +ILYT
Sbjct: 182 IAMAQHRPQHVLLVDRGLAPMAR-TAQRDVDYAPLRTQHLGQQVPVTWLESNASSYILYT 240

Query: 271 SGSTGAPKGVQHTTGGYMVGTYLTTQTVFDLRDDDIYWCTADIGWITGHSYSVYGPLLNG 330
           SG+TG PKGVQ   GGY V    + Q +F  +  + Y+CT+DIGW+ GHSY VYGPL+ G
Sbjct: 241 SGTTGKPKGVQRDVGGYAVALASSMQHIFCGQPGETYFCTSDIGWVVGHSYIVYGPLIAG 300

Query: 331 ATVVMYEGAPNQPDWGRFWDIVQKHRVTILYTAPTAIRSFMQHGDEIPGRYDLASLRLLG 390
              V+YEG P +PD G +W IV+K++VT +++APTAIR   +   E   RYD +SL+ L 
Sbjct: 301 MATVLYEGLPIRPDAGIWWSIVEKYKVTRMFSAPTAIRVLKKQPPECMERYDTSSLKALY 360

Query: 391 SVGEPINPEAWMWYYRVIGGERCPVVDTWWQTETGSIMLTTLPGA--FPSKPGSAGLPMF 448
             GEP++     W   + G  + PV+D +WQTE+G  +++   G    P++ GS G+PM 
Sbjct: 361 LAGEPLDETTSSW---ISGALKVPVIDNYWQTESGWPIISIAKGIDDKPTRLGSPGVPMP 417

Query: 449 GVEPALMTR-DGEEIGDDDGGLLVIKRPW-PSMLRTVYGDDERYRKSYWGEIP-HVYFAG 505
           G   A++    GE  G D  G++ I+ P  P  ++TVYGDDER+  +YW  +P  VY   
Sbjct: 418 GYRLAILDEATGEPCGPDQKGVVAIEGPLPPGCMQTVYGDDERFVNTYWRSLPREVYSTF 477

Query: 506 DGARRDHDGYYTIVGRVDDVLNVSGHRLGTMEIESALVAHPDVSEAAVVGRPDPVKGESV 565
           D   RD DGYY I+GR DDV+NV+GHRLGT EIE ++ +HP+VSE AVVG  D +KG+  
Sbjct: 478 DWGIRDKDGYYFILGRTDDVINVAGHRLGTREIEESISSHPNVSEVAVVGVEDKLKGQVA 537

Query: 566 VAYVLLQDGHT--------ADPAALRAHVSSEIGALARPDAIYIADALPKTRSGKIMRRF 617
            A+ + +  +T        A  A + A V  +IGA+ RP  ++    LPKTRSGK++RR 
Sbjct: 538 FAFAIPKQAYTIATPEQRKALEAEIMAVVDKQIGAVGRPARVFFVSGLPKTRSGKLLRRA 597

Query: 618 LRQLAAGQPVQGDTSTLEDPTVLERLQA 645
           ++ +  G+   GD  T+EDP  LE+++A
Sbjct: 598 IQSICEGRD-PGDLPTIEDPAALEQVRA 624


Lambda     K      H
   0.319    0.137    0.432 

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: 1182
Number of extensions: 71
Number of successful extensions: 8
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: 649
Length of database: 628
Length adjustment: 38
Effective length of query: 611
Effective length of database: 590
Effective search space:   360490
Effective search space used:   360490
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: 54 (25.4 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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