GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Granulicella mallensis MP5ACTX8

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_014265940.1 ACIX8_RS13690 citrate synthase

Query= SwissProt::O34002
         (379 letters)



>NCBI__GCF_000178955.2:WP_014265940.1
          Length = 388

 Score =  285 bits (730), Expect = 1e-81
 Identities = 151/366 (41%), Positives = 223/366 (60%), Gaps = 9/366 (2%)

Query: 8   KGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSELKAF 67
           KGL  V A+ ++I  ++ D   L YRG  + ELA K SFE++ YLLWN  LP  +EL  F
Sbjct: 7   KGLQDVVANESSICFIDGDKGILSYRGIDIHELAEKSSFEEITYLLWNGALPTAAELNDF 66

Query: 68  VNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKAMSL 127
            +   + R++ ++V   +  +     PM+V RT VS+L    A  + +   AN+ K+  L
Sbjct: 67  SHQLAAARQIPDDVIAFLRNVPKTASPMEVLRTTVSLLSIYDADEKSTLHTANIRKSFRL 126

Query: 128 LATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAAPEVVEAFNVSMILYAEH 187
            A    +VA   R R+G+E+++P   L ++ANFLWM  GE+ +    +A +V++IL+A+H
Sbjct: 127 TAQIAMIVAIFDRIRKGKEIVKPDTSLSHAANFLWMLNGEKPSETATKALDVALILHADH 186

Query: 188 SFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGIRKDESLDEA 247
             NASTF ARVI +TL+DLHSA+TGAIGALKGPLHGGANEAVMH   +I        D+A
Sbjct: 187 ELNASTFAARVIAATLSDLHSAITGAIGALKGPLHGGANEAVMHLLYDI--------DKA 238

Query: 248 ATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYDRPEMLGLYNGLE 307
                  +   LA K+K+ GFGHRVY   D R   ++   + + K  + P+   +   +E
Sbjct: 239 GEDPVEHVRKMLANKEKISGFGHRVYTTEDPRATHLRKMSEDLGKDAN-PKWYTMSRQIE 297

Query: 308 AAMEEAKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWTAHIMEQVADNALIRPL 367
             ++E K++  N+D+ +  TY  +G D ++FTP+F  +RI+GW AH++EQ  DN LIRP 
Sbjct: 298 LFVKEEKKLNANVDFYSASTYTTLGIDIDLFTPIFAISRISGWCAHVIEQHDDNRLIRPR 357

Query: 368 SEYNGP 373
           ++Y GP
Sbjct: 358 ADYTGP 363


Lambda     K      H
   0.316    0.130    0.376 

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: 377
Number of extensions: 18
Number of successful extensions: 3
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: 379
Length of database: 388
Length adjustment: 30
Effective length of query: 349
Effective length of database: 358
Effective search space:   124942
Effective search space used:   124942
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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