GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Phaeobacter inhibens BS107

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein

Query= reanno::WCS417:GFF4324
         (428 letters)



>FitnessBrowser__Phaeo:GFF3852
          Length = 409

 Score =  219 bits (559), Expect = 9e-62
 Identities = 142/384 (36%), Positives = 205/384 (53%), Gaps = 29/384 (7%)

Query: 10  AISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAV----DVLKAQVEKDGFVWKDGAVA 65
           +I + +   +SA  A S   +EV HWWTSGGE AAV    D +  Q   +   W DGA+A
Sbjct: 5   SILMTTALSVSATIAQS-ADLEVTHWWTSGGEAAAVTKFADAVNGQTTHN---WVDGAIA 60

Query: 66  GGGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKWDSLLD 124
           G G  TA  ++ SR + G+P    Q+  G   +E    GL+ TD L ++A++E W  +++
Sbjct: 61  GSG-TTARPIIISRILGGDPMAATQLTHGRQAEELIEAGLM-TD-LTELAEQEGWRDIVN 117

Query: 125 K-KVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAG 183
              + D+  YEG    VPVNIH   WLW++ E F KAG++  P    EF AA  KL  AG
Sbjct: 118 PPSLLDSCTYEGRIYCVPVNIHSTQWLWLSHEAFDKAGMSV-PQDWYEFVAAAPKLAEAG 176

Query: 184 FIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVK---ALTELKKV 240
            +PLA G Q WQ    F A+ + ++  D ++K  ++ D G   GP+  K   A+ + +++
Sbjct: 177 IVPLAMGQQGWQQRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDAREL 236

Query: 241 ATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKA 300
           A   +V    QDWNL    VI GKAG QIMGDWA+ E+T A++VAG+DY C+   G ++ 
Sbjct: 237 ARNSNV----QDWNLATNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQI 292

Query: 301 FTYNIDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGF 360
              + D+       D      Q D+A V++ +  Q  F++ KGS+PVR D+         
Sbjct: 293 IDTSGDAFYFPVIDDAEVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGDV--------D 344

Query: 361 DSCAQTAAKDFLADAKTGGLQPSM 384
            S A    K  LA    G + PSM
Sbjct: 345 LSAANDCMKKGLAILADGNVLPSM 368


Lambda     K      H
   0.314    0.131    0.388 

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: 498
Number of extensions: 29
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: 428
Length of database: 409
Length adjustment: 32
Effective length of query: 396
Effective length of database: 377
Effective search space:   149292
Effective search space used:   149292
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: 42 (22.0 bits)
S2: 50 (23.9 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