GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11890 in Phaeobacter inhibens BS107

Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= reanno::WCS417:GFF2332
         (517 letters)



>lcl|FitnessBrowser__Phaeo:GFF2274 PGA1_c23060 ribose import
           ATP-binding protein RbsA
          Length = 503

 Score =  427 bits (1097), Expect = e-124
 Identities = 218/495 (44%), Positives = 324/495 (65%)

Query: 19  EEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAG 78
           E+  +L +  I K FPGV AL  V L + PG V ALMGENGAGKSTLMK++ GI+QPD G
Sbjct: 3   EQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEG 62

Query: 79  EIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMH 138
           +I +  +P+V   PL A+  GI  IHQEL+L   +S+AENI++G        +V+  E+ 
Sbjct: 63  QIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELE 122

Query: 139 RCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198
             T  +L +L++  + + +VG+LSIA +QMVEIA+A++ D+  +I DEPT+++T+ E   
Sbjct: 123 AKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVV 182

Query: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258
           LF +I+DL+ QG GI YI+H+M E+F I D ++V RDG Y G       N +++  MM+G
Sbjct: 183 LFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIG 242

Query: 259 RELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETI 318
           R+L          +G++ L VR L+   +F+DV+F++  GE++G  GL+G+GRT +AET+
Sbjct: 243 RKLDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETL 302

Query: 319 FGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPH 378
           FG+   +SG I LDG  V I+ PH AIE+G +L+ EDRK  GL   ++  +NM +  +  
Sbjct: 303 FGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDD 362

Query: 379 YTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438
                F+   A  A+ +    KL ++TP  +Q +  LSGGNQQK ++ +WL   P +LI+
Sbjct: 363 LKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIV 422

Query: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498
           DEPTRGIDVG+KAEI+ L+  LA++G AVI+ISSE+PEVL ++DR++ M+ G +M T   
Sbjct: 423 DEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTS 482

Query: 499 SEATQEKVMQLASGM 513
            E T+E ++   SG+
Sbjct: 483 EEVTEENLIAAISGL 497



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 59/229 (25%), Positives = 114/229 (49%), Gaps = 5/229 (2%)

Query: 41  DVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGI 100
           DV   VR G V+   G  GAG++ + + + G+  P +G I L G  +   +P  A + GI
Sbjct: 274 DVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGI 333

Query: 101 AMIHQELN---LMPHMSIAENIWIGR-EQLNSLHMVNHREMHRCTAELLARLRINLDPEE 156
           +++ ++     L+  M+  +N+ + + + L +   V          +   +L I     +
Sbjct: 334 SLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWK 393

Query: 157 Q-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVY 215
           Q VGNLS   +Q + I K +S   ++LI+DEPT  I     A + +++ DL +QG  ++ 
Sbjct: 394 QLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIV 453

Query: 216 ITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQL 264
           I+ +M EV  +AD +     G  +    ++ +  ++LI+ + G +  ++
Sbjct: 454 ISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTEKV 502


Lambda     K      H
   0.320    0.136    0.381 

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: 610
Number of extensions: 31
Number of successful extensions: 5
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: 517
Length of database: 503
Length adjustment: 34
Effective length of query: 483
Effective length of database: 469
Effective search space:   226527
Effective search space used:   226527
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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