GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc04259 in Phaeobacter inhibens BS107

Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein

Query= reanno::Smeli:SMc04259
         (411 letters)



>lcl|FitnessBrowser__Phaeo:GFF3852 PGA1_78p00160 putative
           sugar-binding periplasmic protein
          Length = 409

 Score =  514 bits (1324), Expect = e-150
 Identities = 259/402 (64%), Positives = 311/402 (77%), Gaps = 4/402 (0%)

Query: 13  TAALPFGA--ASATDLEVTHWWTSGGEAAAVAELAKAFDA-TGNKWVDGAIAGSGGTARP 69
           T AL   A  A + DLEVTHWWTSGGEAAAV + A A +  T + WVDGAIAGSG TARP
Sbjct: 9   TTALSVSATIAQSADLEVTHWWTSGGEAAAVTKFADAVNGQTTHNWVDGAIAGSGTTARP 68

Query: 70  IMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSLLDSCTIE 129
           I+ISRI GGDPMAATQ  HGRQAEEL++AGLM DLT++A +E W++IV P SLLDSCT E
Sbjct: 69  IIISRILGGDPMAATQLTHGRQAEELIEAGLMTDLTELAEQEGWRDIVNPPSLLDSCTYE 128

Query: 130 GKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEKAGIVPLAVGGQPWQ 189
           G+IYC PVNIHS QWLWLS+ AF +AG+ VP++W EFVAAAP L +AGIVPLA+G Q WQ
Sbjct: 129 GRIYCVPVNIHSTQWLWLSHEAFDKAGMSVPQDWYEFVAAAPKLAEAGIVPLAMGQQGWQ 188

Query: 190 ANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARRMSKGTNVQDWNQA 249
              AF  L V +  ++++ KV  ++D  VAAGP+ AKVF A  DAR +++ +NVQDWN A
Sbjct: 189 QRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDARELARNSNVQDWNLA 248

Query: 250 TNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDAFYFPLLEDE 309
           TNMVITGKAGGQIMGDWAQGEF LA Q AG DY+CLPG+G+N++I T GDAFYFP+++D 
Sbjct: 249 TNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQIIDTSGDAFYFPVIDDA 308

Query: 310 EKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKGLDILAKGNVIQGT 369
           E  +AQ  +AS L+  E QV FNL KGSLPVRGDVDL+AANDCMKKGL ILA GNV+   
Sbjct: 309 EVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGDVDLSAANDCMKKGLAILADGNVLPSM 368

Query: 370 DQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFADIIAAAD 411
           DQ  SAD+Q Q +DL +EF+A+  M   DAQ R+A+IIA AD
Sbjct: 369 DQAFSADTQAQIQDLMAEFWAS-DMAAADAQARYAEIIADAD 409


Lambda     K      H
   0.315    0.131    0.389 

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: 551
Number of extensions: 22
Number of successful extensions: 3
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: 411
Length of database: 409
Length adjustment: 31
Effective length of query: 380
Effective length of database: 378
Effective search space:   143640
Effective search space used:   143640
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: 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 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