GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Pantoea rwandensis LMG 26275

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_002095475.1:WP_084935209.1
          Length = 494

 Score =  421 bits (1081), Expect = e-122
 Identities = 224/490 (45%), Positives = 324/490 (66%), Gaps = 4/490 (0%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L  + I K FPGV+ALD VS  +  G VH LMGENGAGKSTL+K L G Y+PD G + I 
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIK 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G  V+F     ++ +GI++IHQEL  VP +TVAEN+ LG+ P   G+V+  +  +  +E 
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPMKYGFVDHGKLNKQTQEL 125

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
           L  + + L  +  + +LSIA +QMVEI KA+  N+ ++ +DEPTS+L+  E   LF ++R
Sbjct: 126 LNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTIIR 185

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
           DLR   +A+IYISH+MDEI+ + D  +IFRDG  + S+ T E  TR +++++MVGRE++ 
Sbjct: 186 DLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSE-FTRQSLITQMVGRELTQ 244

Query: 245 IYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADH 304
           ++      +G      + +         +F VR+GEI+G  GLVGAGRSE+M  ++G + 
Sbjct: 245 LFPKFNGEIGADVLTVRNLTCKDRFTDINFTVRKGEILGVAGLVGAGRSEVMESLFGMES 304

Query: 305 KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVG 364
              GE+L+DG P+K+ S   AI  G+    EDRK+ G+  + +V EN++I     Y+   
Sbjct: 305 FDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSIVNMPDYVSKA 364

Query: 365 MFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRW-LAEPDLKVVILDE 423
            F+   K A+     I+ L IKTP+  Q I  LSGGNQQK +++RW LA+P  K++ILDE
Sbjct: 365 GFVSHMKMAQDCMEQIRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQP--KILILDE 422

Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483
           PTRGIDVGAK EIY +I +LA RG AI+M+SSELPE+LG+SDR++VM  GRI+G L +++
Sbjct: 423 PTRGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRITGILDKEE 482

Query: 484 ATEQSVLSLA 493
           A ++++LSLA
Sbjct: 483 ANQETILSLA 492



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 64/247 (25%), Positives = 117/247 (47%), Gaps = 8/247 (3%)

Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314
           E    +K   G       S  ++ G +    G  GAG+S LM  + G      G + + G
Sbjct: 7   EAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIKG 66

Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374
           +P++ +   +A+R GI +     +E  +V   TV+ENI +   R  ++ G F+D  K  +
Sbjct: 67  EPVQFQDTMDALRSGISMI---HQELNLVPYMTVAENIWLG--REPMKYG-FVDHGKLNK 120

Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKH 434
                +  L I+  + R  +  LS   QQ   +++ ++  +  +VI+DEPT  +      
Sbjct: 121 QTQELLNRLNIRLKADRM-VGELSIAAQQMVEIAKAVSW-NSDIVIMDEPTSALTETEVA 178

Query: 435 EIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSLAL 494
            ++ +I  L E+G AI+ IS ++ E+  ++D I + R G   G     + T QS+++  +
Sbjct: 179 HLFTIIRDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMV 238

Query: 495 PQSSTAL 501
            +  T L
Sbjct: 239 GRELTQL 245


Lambda     K      H
   0.320    0.136    0.385 

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: 641
Number of extensions: 29
Number of successful extensions: 8
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: 512
Length of database: 494
Length adjustment: 34
Effective length of query: 478
Effective length of database: 460
Effective search space:   219880
Effective search space used:   219880
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: 52 (24.6 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