GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Desulfovibrio vulgaris Miyazaki F

Align Formate-dependent phosphoribosylglycinamide formyltransferase; 5'-phosphoribosylglycinamide transformylase 2; Formate-dependent GAR transformylase; GAR transformylase 2; GART 2; Non-folate glycinamide ribonucleotide transformylase; Phosphoribosylglycinamide formyltransferase 2; EC 2.1.2.- (characterized)
to candidate 8502043 DvMF_2756 phosphoribosylglycinamide formyltransferase 2 (RefSeq)

Query= SwissProt::P33221
         (392 letters)



>FitnessBrowser__Miya:8502043
          Length = 393

 Score =  492 bits (1266), Expect = e-144
 Identities = 248/392 (63%), Positives = 307/392 (78%), Gaps = 1/392 (0%)

Query: 1   MTLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVIN 60
           M  +GT   P+ATR++LLGSGELG+EVAIE  RLGVEVIAVDRY +APAM VAHRSHV++
Sbjct: 1   MVTIGTPNTPSATRILLLGSGELGREVAIEAMRLGVEVIAVDRYPNAPAMQVAHRSHVVS 60

Query: 61  MLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRL 120
           MLDG ALRR++E E+PH IVPEIEAIAT+ L++LE+EG  VVP ARA +LTM+REGIRRL
Sbjct: 61  MLDGAALRRIIEAERPHCIVPEIEAIATETLLELEKEGFRVVPTARAARLTMDREGIRRL 120

Query: 121 AAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKY 180
           AAEEL LPTS YRFA++E+ +REAVA +G PC+VKPVMSSSGKGQ+ +R+   + +AW+Y
Sbjct: 121 AAEELGLPTSPYRFAETEAEYREAVAAVGLPCVVKPVMSSSGKGQSTVRTEADVMKAWEY 180

Query: 181 AQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMS 240
           AQ GGRAG G+VIVEG V FD+EIT LTV    G  FC P+GH Q+DGDYRESWQP  MS
Sbjct: 181 AQTGGRAGGGKVIVEGFVDFDYEITQLTVRHAGGTTFCDPIGHLQKDGDYRESWQPHPMS 240

Query: 241 PLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEF 300
             AL  ++ +A  V  ALGG+G+FGVELF+ GD+V FSEVSPRPHDTG+VTLISQ+LSEF
Sbjct: 241 QAALAESRRMAEAVTGALGGWGIFGVELFIKGDKVYFSEVSPRPHDTGLVTLISQNLSEF 300

Query: 301 ALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVG-ADLQIRLFGKPEID 359
           ALH RA LGLPV  +RQ GPAAS V+L +  S +  +  ++ A+   D  + LFGKPE+ 
Sbjct: 301 ALHARAILGLPVPALRQNGPAASCVVLAEGDSMSPGYHGIEAALAEPDTGLCLFGKPEVH 360

Query: 360 GSRRLGVALATAESVVDAIERAKHAAGQVKVQ 391
           G RR+GVALA   S+ +A  +A+ AA  V+V+
Sbjct: 361 GKRRMGVALALGASIEEARAKARRAAAAVQVE 392


Lambda     K      H
   0.320    0.136    0.390 

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: 468
Number of extensions: 16
Number of successful extensions: 2
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: 392
Length of database: 393
Length adjustment: 31
Effective length of query: 361
Effective length of database: 362
Effective search space:   130682
Effective search space used:   130682
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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