GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_593 Glucose ABC
           transporter, ATP-binding subunit (EC 3.6.3.-)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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