GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Bb in Pseudomonas fluorescens FW300-N2E2

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= uniprot:Q6MNM2
         (347 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889 Glucose ABC
           transporter, ATP-binding subunit (EC 3.6.3.-)
          Length = 386

 Score =  300 bits (768), Expect = 4e-86
 Identities = 165/367 (44%), Positives = 238/367 (64%), Gaps = 30/367 (8%)

Query: 1   MAKIQFSNIKKSFGSA--DVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58
           MA ++  N+ K++G    D LK I+L I  GEFL+LVGPSGCGKSTL+  +AGLE+   G
Sbjct: 1   MATLELRNVNKTYGVGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 59  TISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEIS 118
            I I  + ++ + P++RDIAMVFQSYALYP M+V EN+ FGLK++ +  A I + V  ++
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQAAIDEEVTRVA 120

Query: 119 ELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKR 178
           +LLQI+HLL+RKP +LSGGQ+QRVA+GRAL+R+  + LFDEPLSNLDA LR +MR E+K 
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPE 238
           +H   K+T +YVTHDQ+EA TLGD++AV+KDG+I+Q GTP +IY  P N F+A+FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240

Query: 239 MNFL-------EGAVLEKIPWPEAR-------------KADQILGIRPDAFAL-NQGPLG 277
           MNF+       +G +L  +   +AR               + ILG+RP+   L    P G
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQDAGLEDREVILGMRPEQIMLAGSEPNG 300

Query: 278 TQEVALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMK--QTLPLKIDLTKAH 335
              +     ++ ++E  G   ++   L  N+ ++      + + +  +TL L+ D +K  
Sbjct: 301 LPTIRA---EVQVTEPTGPDTLVFVNL--NDTKVCCRLAPDVAPQPGETLTLQFDPSKVL 355

Query: 336 LFDKKTG 342
           LFD ++G
Sbjct: 356 LFDAQSG 362


Lambda     K      H
   0.318    0.136    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: 361
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 347
Length of database: 386
Length adjustment: 30
Effective length of query: 317
Effective length of database: 356
Effective search space:   112852
Effective search space used:   112852
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 (21.7 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 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