GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Collinsella tanakaei YIT 12063

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_009142044.1 HMPREF9452_RS10150 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_000225705.1:WP_009142044.1
          Length = 564

 Score =  402 bits (1034), Expect = e-116
 Identities = 230/561 (40%), Positives = 330/561 (58%), Gaps = 21/561 (3%)

Query: 14  EHLDLELKERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFA 73
           E L  ELK   ++  GDE A+ D F++DL FGT G+RG IGAGTNRMNIYTV +A+ GFA
Sbjct: 18  EELLAELKA--MQEAGDEDAITDAFFQDLAFGTAGLRGTIGAGTNRMNIYTVGRATQGFA 75

Query: 74  AYISKQGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVR 133
            Y++K  E      V IA DSR+K   F    A  LA  G+ +YV+ ++ P P LS+A R
Sbjct: 76  DYLNKAFENPT---VAIARDSRNKGELFVKTTAAILAANGVTSYVYPKISPVPTLSWATR 132

Query: 134 QLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDEENK 193
            L   GGI +TASHNP  YNGYK YG DG Q+  + AD +   +NA +    I   + + 
Sbjct: 133 YLKCSGGICMTASHNPAPYNGYKAYGPDGCQITSEAADAISAAMNACDPFKDIKTMDFDV 192

Query: 194 LKEKGLIKIIGEDIDKVYTEKLTSISVHPELSEEV---DVKVVFTPLHGTANKPVRRGLE 250
             E+GL+K I +++   Y + +T  SV+    E++    +K+V+TPL+GT   PV   L 
Sbjct: 193 AVEQGLVKWIDDEVLDAYYDAVTDKSVNNLTDEQIANAPLKLVYTPLNGTGLIPVTTVLN 252

Query: 251 ALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLG 310
            +G  ++TVV EQ  PD +F T   PNPE   A +  I L +E   D+L+ATDPDADR+G
Sbjct: 253 KVGITDITVVPEQRDPDGDFPTCPYPNPEIREAMQKGIDLCQEVKPDLLLATDPDADRVG 312

Query: 311 IAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFG 370
           +A   D   YT+LTGN+ G LLL Y+   + ++G    + V + TIV+S +  A+A+ +G
Sbjct: 313 VACA-DGDDYTLLTGNEMGVLLLDYICKMRAERGEDLSSKVAVTTIVSSAMVDALAAEYG 371

Query: 371 LDTIDTLTGFKFIGEKIKEYEASGQY-TFQFGYEESYGYLIGDFARDKDAIQAALLAVEV 429
            +    LTGFK+IG+ I     +G+   F FG+EESYGYL GD  RDKDA+ A++L  ++
Sbjct: 372 FELRRCLTGFKYIGDIITGLSDAGEVDRFIFGFEESYGYLSGDHVRDKDAVNASMLICQM 431

Query: 430 CAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAG 489
             +YK QG +L EA+ +L+ ++G+Y     SL+  G  GA ++  I+ S R   P ++AG
Sbjct: 432 AQYYKLQGKNLVEAMRDLYEKHGYYHNKTVSLSYPGADGAAKMAGIMKSLRSEAPAEIAG 491

Query: 490 KQVVTAEDYAVSKRTLLTESKEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAV 549
            +V    DYA                LP ++V+++ LE G+   +RPSGTEPK+K Y   
Sbjct: 492 SKVEAVVDYATCVN-----------GLPAADVIEFDLEGGNKAIVRPSGTEPKIKLYIFA 540

Query: 550 KGSSLEDSEKRLAVLSEDVMK 570
           KG     ++  +A + ED  K
Sbjct: 541 KGEDAAAADALIAAIEEDGRK 561


Lambda     K      H
   0.313    0.133    0.371 

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: 745
Number of extensions: 35
Number of successful extensions: 6
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: 581
Length of database: 564
Length adjustment: 36
Effective length of query: 545
Effective length of database: 528
Effective search space:   287760
Effective search space used:   287760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 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