GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2274
          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:

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