GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Pantoea rwandensis LMG 26275

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_002095475.1:WP_084935209.1
          Length = 494

 Score =  171 bits (432), Expect = 4e-47
 Identities = 89/254 (35%), Positives = 148/254 (58%), Gaps = 6/254 (2%)

Query: 8   IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67
           +  +GI K F  V AL  VS+ + PG  H L+G+NGAGKST +K + G+++P KG I  +
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIK 65

Query: 68  GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRI 127
           G+P+ F D  DA+ +GI+ +HQ L ++P M+V+ N ++G EP++        DH   N+ 
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPMK----YGFVDHGKLNKQ 121

Query: 128 TMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANV 187
           T E + ++ I L+  D+ VG LS   +Q V IA+AV + + ++I+DEPTSAL   + A++
Sbjct: 122 TQELLNRLNIRLKA-DRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHL 180

Query: 188 LATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247
              I  +R+QG A+++I+H +     + D  ++   G  +G+    + + + L   M  G
Sbjct: 181 FTIIRDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMV-G 239

Query: 248 QELATLEGSLGGTV 261
           +EL  L     G +
Sbjct: 240 RELTQLFPKFNGEI 253



 Score = 97.1 bits (240), Expect = 7e-25
 Identities = 63/220 (28%), Positives = 110/220 (50%), Gaps = 8/220 (3%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85
           ++  V  GE   + G  GAG+S  ++++ G+     G++L +G P+    P  AI  G+A
Sbjct: 272 INFTVRKGEILGVAGLVGAGRSEVMESLFGMESFDSGEVLIDGVPVKIDSPSTAIEKGMA 331

Query: 86  TV---HQHLAMIPLMSVSRNFFMGNEP--IRKIGPLKLFDHDYANRITMEEMRKMGINLR 140
            +    +   +  ++SV  N  + N P  + K G      H    +  ME++RK+ I   
Sbjct: 332 FLTEDRKKSGLFLVLSVMENMSIVNMPDYVSKAG---FVSHMKMAQDCMEQIRKLNIKTP 388

Query: 141 GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVA 200
             DQ +  LSGG +Q V IAR +    K+LILDEPT  + V   A +   I ++  +GVA
Sbjct: 389 TMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDVGAKAEIYRLISELANRGVA 448

Query: 201 VVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240
           ++ ++  +   L + DR  V++ G+  G   + + + E +
Sbjct: 449 IIMVSSELPEILGMSDRVMVMHGGRITGILDKEEANQETI 488


Lambda     K      H
   0.321    0.137    0.395 

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: 298
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 494
Length adjustment: 29
Effective length of query: 232
Effective length of database: 465
Effective search space:   107880
Effective search space used:   107880
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 (21.9 bits)
S2: 49 (23.5 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