GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Herbaspirillum seropedicae SmR1

Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  166 bits (420), Expect = 9e-46
 Identities = 89/245 (36%), Positives = 142/245 (57%), Gaps = 3/245 (1%)

Query: 2   SMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61
           S S P+I ++ + K F  V+AL     ++  GE H L+G+NGAGKST +K +SGV++   
Sbjct: 17  SSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS 76

Query: 62  GDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDH 121
           GDIL +G+P+   +PR A A GI  +HQ L ++  +S ++N F+G EP + +G     D 
Sbjct: 77  GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMG--LFIDE 134

Query: 122 DYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGV 181
           D  NR       +M +++  P   VG L+   +Q V IA+A+ F ++VLI+DEPT+AL  
Sbjct: 135 DELNRQAAAIFARMRLDM-DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193

Query: 182 RQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQ 241
            + A +   I  ++ QGV +V+I+H +     + DR +V+  GK + T    + S + + 
Sbjct: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253

Query: 242 DMMAG 246
            MM G
Sbjct: 254 SMMVG 258



 Score = 78.2 bits (191), Expect = 3e-19
 Identities = 54/225 (24%), Positives = 96/225 (42%), Gaps = 5/225 (2%)

Query: 22  ALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIA 81
           A+  VS  +  GE     G  GAG++   + + G      G+I+  G       P DA+A
Sbjct: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347

Query: 82  AGIATVHQ---HLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGIN 138
            GI  + +   H  +   M V  N  + +  + +   +   D           +R++ I 
Sbjct: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSS--MGRFTRVGFMDQRAIREAAQMYVRQLAIK 405

Query: 139 LRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQG 198
               +Q    LSGG +Q + IA+ +     +L  DEPT  + V   + +   +D + +QG
Sbjct: 406 TPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465

Query: 199 VAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243
            A+V I+  +   L +  R  V+  G+  G   R D + E++  +
Sbjct: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510


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: 315
Number of extensions: 14
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: 520
Length adjustment: 30
Effective length of query: 231
Effective length of database: 490
Effective search space:   113190
Effective search space used:   113190
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 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