GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039
          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.

Links

Downloads

Related tools

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