GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Klebsiella michiganensis M5al

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

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



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  302 bits (773), Expect = 1e-86
 Identities = 167/361 (46%), Positives = 229/361 (63%), Gaps = 11/361 (3%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           M+ + LRNV K +G  +  TL  + L I+DGEF + VGPSGCGKSTL+  IAGLE +S G
Sbjct: 1   MSNIRLRNVTKRFGSTV--TLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEG 58

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            +L+ D  ++ + P  R +AMVFQSYALYP M+V +N+ +GLK+ K+P  EI  +V  V+
Sbjct: 59  EVLIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVA 118

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           K LQ+ HLL RKP QLSGGQ+QRVA+GRA+ R P++++FDEPLSNLDA+LRVEMR  +  
Sbjct: 119 KTLQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAK 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           +H  LKTT VYVTHDQ+EAMTL DK+ VM  G ++Q G+P  +Y NP N FVA FIGSP 
Sbjct: 179 LHHELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPK 238

Query: 241 MNFIPLRLQR-KDGRLLALLDSGQARCELPLGMQDAGLE-DREVILGIRPEQIILANGEA 298
           MNF+P  +   + G+L   +        L L +  + L+    V LGIRPE +   + + 
Sbjct: 239 MNFLPATVTAWQPGQLSVKMAQDH---NLTLNITTSPLQPGAAVTLGIRPEHL---STDV 292

Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVN-LNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLF 357
           N    +  + +V E  G +T +F        V   L  DV     + +++ FD    ++F
Sbjct: 293 NIGTVVEFQCEVVERLGNNTYLFGQCYGHDNVKILLPGDVHFRPWQKISVAFDDRYCMVF 352

Query: 358 D 358
           D
Sbjct: 353 D 353


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: 397
Number of extensions: 17
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: 386
Length of database: 369
Length adjustment: 30
Effective length of query: 356
Effective length of database: 339
Effective search space:   120684
Effective search space used:   120684
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:

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