GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Herbaspirillum seropedicae SmR1

Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS22730 HSERO_RS22730 sugar ABC transporter substrate-binding protein

Query= uniprot:A0A165KPY4
         (416 letters)



>FitnessBrowser__HerbieS:HSERO_RS22730
          Length = 446

 Score =  223 bits (568), Expect = 9e-63
 Identities = 134/400 (33%), Positives = 200/400 (50%), Gaps = 11/400 (2%)

Query: 19  SASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSAMTVLKSRVISG 78
           + + G ++VLH+WTS  E +++  +   +  +   WRD A+ GG G  A  VLKS V++ 
Sbjct: 48  ATATGSLQVLHWWTSASERQAINVVVNQLAKQDIQWRDVAIPGGAGMGAAKVLKSMVLAN 107

Query: 79  NPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMKYKGAYVAAPVNVH 138
             P   Q  G    EWA  G+L  +D +A    W++ +   V  ++   G  VAAP+ +H
Sbjct: 108 RAPEVTQLNGVVFGEWADLGLLLELDNVAVQGNWEKQMFPTVWSLLNNHGHVVAAPLGIH 167

Query: 139 RVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNWQDFTTFESVVL 198
           R+N ++ +    K+  ++  PKTWDEF     KL+ +G+VP+A   + WQ  T FE++ L
Sbjct: 168 RINSLYYNVAVFKRYNLSP-PKTWDEFDQIVKKLQGSGVVPLAQSAEAWQLATLFENLAL 226

Query: 199 GVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWNLATAMLIQGKA 258
              G  +Y+   V++   A     M   L+  R + G        R W      ++ G+A
Sbjct: 227 AESGPAYYRKLFVEMSPAAYLDARMLHILKRLRALAGAMAQPVRERPWTEVARSMVSGEA 286

Query: 259 GFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLKDAAAQKAQSDL 318
              +MGDWAKGE  A G    + F CA APG+     ++ D+  +F   + A Q  Q  L
Sbjct: 287 AMLIMGDWAKGELNAWGMEVDQQFGCAPAPGTGEYHLYSTDTLAMF-AGNYAHQPMQETL 345

Query: 319 ASSIMSPAFQEVFNLNKGSIPV-RAGQPMDKFDDCAKASAKDFVDTAKSGGL--VPSAAH 375
           A   MSPA Q  +N  KGSIPV RA  P    D CA+ S + F      G +   PS  H
Sbjct: 346 ARLTMSPAVQSEYNRIKGSIPVLRAADP--HMDRCARDSWRTF----SKGPMWQAPSLVH 399

Query: 376 GMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKT 415
            MA    T+ AI   V +F+ D  +S   A K++A  A+T
Sbjct: 400 RMATDDTTKDAIVAEVQRFFMDRSISEEQAQKRLATIART 439


Lambda     K      H
   0.315    0.128    0.383 

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: 501
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 416
Length of database: 446
Length adjustment: 32
Effective length of query: 384
Effective length of database: 414
Effective search space:   158976
Effective search space used:   158976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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