GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halioglobus japonicus S1-36

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_084199337.1 C0029_RS09615 AMP-binding protein

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_002869505.1:WP_084199337.1
          Length = 1803

 Score =  252 bits (643), Expect = 1e-70
 Identities = 168/512 (32%), Positives = 254/512 (49%), Gaps = 71/512 (13%)

Query: 224 TGVESVIVLPRLGLKDVPMTEGRDYWWNKLM----QGIPPNA------------------ 261
           +GV+ VIV+    L ++   EGRD W   ++      I  NA                  
Sbjct: 328 SGVQKVIVVRHADLPEISWHEGRDLWAEDILIQAEATILSNAGLQKRSELMALGDTELTQ 387

Query: 262 ----YIEPEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIR-DDDIF 316
                ++P PV ++ P FI+YTSG+TGKPKG+VH  GG+   V  + K  FD R  +DI 
Sbjct: 388 ALWRSVKPVPVSADFPLFIIYTSGSTGKPKGVVHVHGGYTAGVSYSTKISFDARAGEDII 447

Query: 317 WCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAI 376
           W  AD GW+TG SY++   L    T V+ EG P +P   R+ SIIERYGVTIF    T +
Sbjct: 448 WVIADPGWITGQSYLISAALTNRLTSVVTEGPPTFPNAGRFASIIERYGVTIFKAGVTFL 507

Query: 377 RMFMRYGEEW--PRKHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETG 434
           +  +   +      ++  S++R+     EP +P   R+A  ++  + +   +++W TE G
Sbjct: 508 KGIISNPQNRLDVERYSRSSVRVATFCAEPTSPSVQRFAMDLVTPQYI---NSYWATEHG 564

Query: 435 GIVISHAPGLYLVPMKPGTNGPPLPGFEVDVVDENGNP----------APPGVKGYLVIK 484
           GIV +H  G   +P++      PLP    D+   N  P          A P  KG +VI 
Sbjct: 565 GIVWTHPYGNAEMPLRADAQTYPLPWIFGDIWIGNSEPDETGRVTYSQARPDEKGEIVIT 624

Query: 485 KPWPGMLHGIWGDP------------ERYIKTYWSRFPG-------MFYAGDYAIKDKDG 525
           +P+P +   IWGDP            ER+  TY+ R+          +  GD+A +  +G
Sbjct: 625 RPYPYLARTIWGDPDNVNSDEWMGDIERFKATYFGRYRSDSGEPEYTYVQGDFARRYTNG 684

Query: 526 YIWVLGRADEVIKVAGHRLGTYELESALIS------HPAVAESAVVGVPDAIKGEVPIAF 579
              + GR+D+VI V+GHR+GT E+E A++          V    V+G P   KG  P+AF
Sbjct: 685 SYSLHGRSDDVINVSGHRMGTEEIEGAILKDRQLNPESKVGNCIVIGAPHQDKGLTPLAF 744

Query: 580 V--VLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKIMRRLLKAVAT 637
           +  V +Q ++  DE  + L E V+   G +A P+    V   P+TRSGK +RR LKA+  
Sbjct: 745 ILPVARQSLSSDDE--RHLAELVQTEKGSLAVPSAFLCVDAFPETRSGKYLRRFLKAIVL 802

Query: 638 GAPLGDVTTLEDETSVEEAKRAYEEIKAEMAR 669
              LGD +TL +   + + +R  E+ + +  R
Sbjct: 803 DQELGDTSTLRNPECLPKIRRVVEQWRRQEDR 834



 Score =  100 bits (248), Expect = 8e-25
 Identities = 64/185 (34%), Positives = 97/185 (52%), Gaps = 8/185 (4%)

Query: 52  AKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHVKTWRKNKLAIEWEGEPVDE 111
           A  L W +PW + LD S+ PFY+WF G   N ++  +DRHV     +++A  +EG+  D 
Sbjct: 77  ADALAW-QPWQQALDESSAPFYRWFSGAMTNAAFNELDRHVLAGHGDEIAFYYEGDRWDP 135

Query: 112 -----NGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLYLPMVPELPITMLAA 166
                 G P     ++  +L       A  L +  G+ KGD+I + +P + E  +   AA
Sbjct: 136 ALNAGKGGPVQHNAISRRELLLRSVIAAQALLE-LGLVKGDRIAINMPNILEQIVWTEAA 194

Query: 167 WRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRLKEV-VDAALEKATG 225
            RIG I + VF GFS   LA+RI ++ + +VITADG  R   +V  KE   D AL+    
Sbjct: 195 KRIGVIYTPVFGGFSDKTLADRIENAGASVVITADGASRNAELVPFKEAYCDPALDLYIS 254

Query: 226 VESVI 230
           ++S +
Sbjct: 255 LKSAL 259


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: 3036
Number of extensions: 151
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 670
Length of database: 1803
Length adjustment: 46
Effective length of query: 624
Effective length of database: 1757
Effective search space:  1096368
Effective search space used:  1096368
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: 58 (26.9 bits)

This GapMind analysis is from Sep 24 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