GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Methanospirillum stamsii Pt1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_109940435.1 DLD82_RS07210 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_003173335.1:WP_109940435.1
          Length = 630

 Score =  546 bits (1408), Expect = e-160
 Identities = 293/649 (45%), Positives = 416/649 (64%), Gaps = 21/649 (3%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           M A E +  + +V+ P   + + A I     Y  L  E E+D + FW R A +LL W K 
Sbjct: 1   MPAEEVLKPDQKVYYPDPSYQNSALIRD---YDELYREFEKDPDAFWRRIASDLL-WFKQ 56

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           +  V    + P   WF + ELN +YNCL+R++ N   +KVAI +  ++G    +TY +L+
Sbjct: 57  WDTVRTWDH-PHASWFTNAELNITYNCLERHVNNDRRNKVAIFWAGENGKERILTYYQLY 115

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
             V R  N LK+LG+RKGDRV IY+P   E VV+M ACAR+GA H+VVF G+ AK+L ER
Sbjct: 116 KDVMRMGNALKSLGVRKGDRVCIYLPGIPELVVSMLACARIGAVHTVVFAGYGAKALNER 175

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           +   GA  +ITAD  +R G ++PLK I ++AL       V  VI+ R    KV   +  +
Sbjct: 176 ITGAGAKIVITADASVRRGGSIPLKPIVEEALI--HAPTVEKVIILRTQEPKVGLLDDFE 233

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
              E++ +     CE E V++E PLF+LYTSG+TG PKG+ H+ GGY++ A  T K+   
Sbjct: 234 LDYEELISQADRNCEPEHVNSEDPLFILYTSGTTGAPKGIVHTAGGYMVGAYYTTKYVLT 293

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
           ++ +D++WCTAD GW+TGHTY  YGPL  G T  + E  P YP+AG +W +I  + V+IF
Sbjct: 294 LRENDVYWCTADPGWITGHTYGIYGPLLVGGTIFLTEYTPDYPDAGIWWKLIEEYGVTIF 353

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIR  ++  E       ++YDLSSLRLLG+VGEP+NPEA+ W+YK+IG + CPI+
Sbjct: 354 YTAPTAIRMFMRMGEE----WSEKYDLSSLRLLGSVGEPLNPEAFEWFYKHIGKKNCPIL 409

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETG HMIT + G  P+ PG    P+PG++A +V+E G  VP G  G L +K PW
Sbjct: 410 DTWWQTETGMHMITTMVG-LPMKPGFAGKPIPGVVATVVNEEGDPVPPGTNGFLAIKEPW 468

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P+M++T++ + ER+R+ +   + G   Y + D ++ D+D GY  ++GR DD++ V+GH +
Sbjct: 469 PSMMKTVYQNDERYRQYWNFGKYG--YYSSNDIAMMDED-GYIMLLGRSDDIIIVAGHNV 525

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRS-RPTGEEAVKIATELRNWV 599
           GT EIESALVS+  VAEAA +G+PD + G  I AFV+L+    PT     K+  +L+  V
Sbjct: 526 GTAEIESALVSHSAVAEAAAIGKPDPLKGNIIKAFVILRNGVSPT----PKLIHDLKYHV 581

Query: 600 GKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLE 648
              +GPI+ P ++ F DNLPKTRSGKIMRR+L++   G +   D STL+
Sbjct: 582 RIMLGPISVPAELDFVDNLPKTRSGKIMRRVLKAQEMGID-PGDVSTLD 629


Lambda     K      H
   0.319    0.136    0.422 

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: 1240
Number of extensions: 70
Number of successful extensions: 7
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: 660
Length of database: 630
Length adjustment: 38
Effective length of query: 622
Effective length of database: 592
Effective search space:   368224
Effective search space used:   368224
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: 54 (25.4 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