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_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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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