Alignments for a candidate for prpE in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Marivita geojedonensis DPG-138

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_085636903.1 MGEO_RS10460 acetate--CoA ligase

Query= BRENDA::Q99NB1
         (682 letters)



>NCBI__GCF_002115805.1:WP_085636903.1
          Length = 582

 Score =  296 bits (757), Expect = 2e-84
 Identities = 195/569 (34%), Positives = 284/569 (49%), Gaps = 34/569 (5%)

Query: 94  GWFLGGQLNVSVNCLDQHVQKSPET-IALIWERDEPGTEVRITYRELLETTCRLANTLKR 152
           GW   G +N++   LD+HV       IA+ W   +  T+  +TY +L E   R AN L  
Sbjct: 41  GW--KGGINIAHEALDRHVADGHGAQIAIKWLGKDGSTQ-DLTYTDLTELASRFANVLVD 97

Query: 153 HGVHRGDRVAIYMPVSPLAVAAMLACARIGAIHTVVFAGFSAESLAGRINDAKCKAVITF 212
           HG+ +GD V   M   P   AA L   + G I T +F+ F  E +  R+   K   ++T 
Sbjct: 98  HGLRKGDSVFALMGRVPELYAAALGALKAGLIFTPLFSAFGPEPIRTRMEIGKANVLVT- 156

Query: 213 NQGLRGGRVVELKKIVDEAVKSCPTVQHVLVAHRTDTKVPMGSLDIPLEQEMAKEAPVCT 272
                       K+ + +     PT++ VL+        P     I L   MA  A    
Sbjct: 157 -------TASIYKRKISKWRDEIPTLKLVLIV---GDDAPEDC--IALGPSMASAATAFE 204

Query: 273 PESMSSEDMLFMLYTSGSTGTPKGLVHTQAGYLLYAAMTHKLVFDYQPGDVFGCVADIGW 332
               + ED   + +TSG+TG PKG VH     ++Y A +        PG ++ C AD GW
Sbjct: 205 TVRTAPEDPALIHFTSGTTGKPKGAVHVHNA-VIYHAFSGNYALRLSPGTIYWCTADPGW 263

Query: 333 ITGHSYVVYGPLCNGATTVLFESTPVYPDAGRYWETVQRLKINQFYGAPTAVRLLLKYGD 392
           +TG +Y +  PL N  T ++ E+     D  R++ T+++ ++  +Y APTA+R++++ G+
Sbjct: 264 VTGTTYGIISPLVNRVTMLVDEAEF---DIDRWYGTIEKERVEVWYSAPTAIRMMMRAGN 320

Query: 393 AWVKKYDRSSLRTLGSVGEPINHEAWEWLHKVVGDGRCTLVDTWWQTETGGICIAPRPSE 452
           A   KYD SSL  L SVGEP+N EA  W  +V G       D WWQTETGGI IA  P  
Sbjct: 321 ATAAKYDFSSLVFLASVGEPLNPEAVIWSKEVFGQ---PFHDNWWQTETGGIMIANCP-- 375

Query: 453 DGAEILPGMAMRPFFGIVPVLMDEKGN-VLEGGDVS-GALCISQAWPGMARTIYGDHQRF 510
            GAE+ PG   RP  GI   ++ +  + ++E GD   G L +   WP M R    +  R+
Sbjct: 376 -GAEVRPGSMGRPLPGIEAAIVTQANDGMVELGDGEIGELALRPGWPSMMRAYLNEEARY 434

Query: 511 VDAYFRAYPGYYFTGDGAHRTEGGYYQITGRMDDVINISGHRLGTAEIEDAMADHPAVPE 570
              +     G+Y +GD A R + GY+   GR DD+I  SGH +G  E+E A+ +H AV E
Sbjct: 435 QKCF---RDGWYLSGDLAMRDKDGYFWFVGRADDLIKTSGHLIGPFEVESALIEHEAVAE 491

Query: 571 TAVIGYPHDIKGEAAFAFIVLKDNISDENMVVNELKLSVATKIAKYAVPDQILVVKRLPK 630
             VIG P +  GE   A++ L      ++ +   ++     K+     P +I+  K LPK
Sbjct: 492 AGVIGVPDETAGELVKAYVTLNPGFQPDDDLEQSIRGHARKKLGPAVAPREIVFRKTLPK 551

Query: 631 TRSGKVMRRLLRKIITSRGQDLGDTTTLE 659
           TRSGK+MRRLL+      G   GD +TLE
Sbjct: 552 TRSGKIMRRLLK--ARELGLPEGDISTLE 578


Lambda     K      H
   0.320    0.136    0.421 

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: 1012
Number of extensions: 61
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: 682
Length of database: 582
Length adjustment: 38
Effective length of query: 644
Effective length of database: 544
Effective search space:   350336
Effective search space used:   350336
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 24 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 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