GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PfGW456L13_1897 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039 Various
           polyols ABC transporter, ATP-binding component
          Length = 367

 Score =  314 bits (805), Expect = 2e-90
 Identities = 173/361 (47%), Positives = 243/361 (67%), Gaps = 9/361 (2%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA L+++N+ K +  G    +K I+L+++D EF++ VGPSGCGKSTL+  IAGLE +SGG
Sbjct: 1   MANLKIKNLQKGF-EGF-SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            I +D  DI+ +SP  RD+AMVFQ+YALYP MSVR N++F L +  +  AE++++V+  +
Sbjct: 59  TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAA 118

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           ++L++  +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+  
Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           +H+ L+ T +YVTHDQ+EAMT+ DKV V+  G I+Q G+P D+Y+ PANLFVA F+G+P 
Sbjct: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238

Query: 241 MNFIPLRLQRKDGRLLAL-LDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEAN 299
           M F+  ++ R D +   + LD+G  R  LPLG +   +    V LGIRPE + LA     
Sbjct: 239 MGFLKGKITRVDSQGCEVQLDAG-TRVSLPLGGRHLSV-GSAVTLGIRPEHLELAK---P 293

Query: 300 GLPTIRAEVQVTEPTGPDTLVFV-NLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358
           G   ++    V+E  G DT   V   +   +  R+  D+A   GETL+L  D     LFD
Sbjct: 294 GDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFD 353

Query: 359 A 359
           A
Sbjct: 354 A 354


Lambda     K      H
   0.319    0.138    0.393 

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: 417
Number of extensions: 19
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: 386
Length of database: 367
Length adjustment: 30
Effective length of query: 356
Effective length of database: 337
Effective search space:   119972
Effective search space used:   119972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 preprint 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