Alignments for a candidate for prpE in Methanobacterium lacus AL-21

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Methanobacterium lacus AL-21

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013645469.1 METBO_RS09375 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000191585.1:WP_013645469.1
          Length = 633

 Score =  610 bits (1572), Expect = e-179
 Identities = 314/644 (48%), Positives = 436/644 (67%), Gaps = 21/644 (3%)

Query: 7   VMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLD 66
           ++ E R+F P      +A + + E       E  +++E +W   A EL  W + + KVLD
Sbjct: 8   LLDEKRIFKPDVETVERAHVKNWENEI----EKGKNFEAYWEEKAEEL-EWFEKWDKVLD 62

Query: 67  QSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRF 126
           ++N PFY+W+ +G++N +YN +DR +     ++VAI++  + G   ++TY EL+ +V + 
Sbjct: 63  ETNKPFYQWYVNGKINLTYNAVDRWIYTEKRNQVAILYINERGDEEKLTYYELYRQVNKM 122

Query: 127 ANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGA 186
           ANGLK LG+ KGD V +Y+PM  E +++M ACA++GA HSVV+ G S  +  ER+ D  A
Sbjct: 123 ANGLKNLGVNKGDTVSMYLPMCPELLISMLACAKIGAVHSVVYSGLSVGAFVERMNDANA 182

Query: 187 VALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTE--GRDRWME 244
             LITAD   R GK + LK I+D+AL    C  +  VIV + TG ++  ++  GR+ + +
Sbjct: 183 KILITADGTYRRGKIINLKKISDEALLQ--CPTIETVIVLKHTGSEINVSDLSGREIFYD 240

Query: 245 DVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPD 304
               G+P  CE E + AE PLF+LYTSGSTGKPKGV H+TGGY++    T+K  FDI+ D
Sbjct: 241 RFLEGEPAECEPEWMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVATTLKNIFDIQKD 300

Query: 305 DLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAP 364
           DL+WCT DIGW+TGH+Y+ YGPL  G T +V+EG P YP+ G +W +I +H V+ FYTAP
Sbjct: 301 DLWWCTGDIGWITGHSYVIYGPLLLGTTTIVYEGAPDYPDPGAWWKIIEKHGVTKFYTAP 360

Query: 365 TAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFW 424
           TAIR L++        +P  Y+LSSLR+LGTVGEPINPEAWMW+YKN+G E+ PI+DT+W
Sbjct: 361 TAIRHLMRFGNK----YPNIYNLSSLRILGTVGEPINPEAWMWFYKNVGKEKTPIMDTWW 416

Query: 425 QTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMI 484
           QTETG H+I+PLP A  L PGS T P PG+ A +VDE G+ VP G GG LV+K+PWPAM 
Sbjct: 417 QTETGMHLISPLPSA-HLKPGSATKPFPGVDADVVDEDGNPVPLGKGGYLVIKKPWPAMF 475

Query: 485 RTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTME 544
           RT++ D ERF++ Y+ +  G  +Y AGD + +D+D GYF I GR DDVL ++GHR+GT E
Sbjct: 476 RTLYEDEERFQQVYWNQIPG--VYKAGDMARKDED-GYFWIQGRSDDVLKIAGHRVGTAE 532

Query: 545 IESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIG 604
           +ESA VS+P VAEAAV+G+ D + G+ I AF++LK      +   K+  EL   V  E+G
Sbjct: 533 VESAFVSHPAVAEAAVIGKSDPIKGQVIKAFLILKEGY---QLKTKLIEELNKHVRYELG 589

Query: 605 PIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLE 648
           P+A   ++   + LPKTRSGKIMRRLLR+   GE++  DTSTLE
Sbjct: 590 PVAVIGEMEQVEKLPKTRSGKIMRRLLRAKESGEDL-GDTSTLE 632


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: 1268
Number of extensions: 67
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: 660
Length of database: 633
Length adjustment: 38
Effective length of query: 622
Effective length of database: 595
Effective search space:   370090
Effective search space used:   370090
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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