GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22730 HSERO_RS22730 sugar ABC
           transporter substrate-binding protein
          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 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