GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas fluorescens FW300-N1B4

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Pf1N1B4_593 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_593
          Length = 386

 Score =  290 bits (742), Expect = 4e-83
 Identities = 151/322 (46%), Positives = 213/322 (66%), Gaps = 33/322 (10%)

Query: 17  VGSLQLKTIRKAFGSH--EVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSG 74
           + +L+L+ + K +G+   + LK I+L + DGEF+I VGPSGCGKSTL+  IAGLE+ + G
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELKINDGEFLILVGPSGCGKSTLMNCIAGLENISGG 60

Query: 75  SVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAA 134
           ++ +D  ++  ++P  R IAMVFQSYALYP ++V+DN+  GLK   +P AEI+E+VA+ A
Sbjct: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVA 120

Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194
            +L +E  L+R+P +LSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDA LRV  R E+  
Sbjct: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQ 254
           +H+ LK T +YVTHDQ+EAMTL DK+ V+  G I+Q G+P ++YN PANLFVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240

Query: 255 MNFIE----------AAKLGDGEAK-----------------TIGIRPEHIGLSRESGDW 287
           MNFI            A L  G+A+                  +G+RPE I L+    + 
Sbjct: 241 MNFIPLRLQRKDGRLVALLDSGQARCELPLGMQDAGLEDREVILGMRPEQIVLAGSEPNG 300

Query: 288 ----KGKVIHVEHLGADTIIYI 305
               + +V   E  G DT++++
Sbjct: 301 LPTIRAEVQVTEPTGPDTLVFV 322


Lambda     K      H
   0.320    0.137    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: 358
Number of extensions: 15
Number of successful extensions: 1
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: 352
Length of database: 386
Length adjustment: 30
Effective length of query: 322
Effective length of database: 356
Effective search space:   114632
Effective search space used:   114632
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 (21.8 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:

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