GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Collimonas pratensis Ter91

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_061936170.1 CPter91_RS01725 ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>NCBI__GCF_001584185.1:WP_061936170.1
          Length = 327

 Score =  218 bits (555), Expect = 2e-61
 Identities = 123/324 (37%), Positives = 190/324 (58%), Gaps = 18/324 (5%)

Query: 6   KKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGG 65
           +K   ++   L +LV L +  ++ +  F T  N  ++  Q+    +L IG T VII+GG 
Sbjct: 5   QKDLIQKFAALGSLVVLGLVFSLTSDAFFTLNNGMSVALQVTSIAILGIGATCVIITGG- 63

Query: 66  AIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIIT 125
            IDLS GS++AL GV+ A ++  G+PV + ++  L      G  +GL +T+L++P FI T
Sbjct: 64  -IDLSVGSVLALAGVIAAMVVKAGMPVPVGMLCGLAVGAVCGGLNGLCITQLKLPPFIAT 122

Query: 126 LGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKI----------------PIPVWI 169
           LG + +ARG+A  +T   P+ GLP  F  +G G   +I                P PV +
Sbjct: 123 LGMMLVARGVALQVTGARPVSGLPEEFGTLGNGTLFRIVKETTGPFPDVVFPGIPYPVIL 182

Query: 170 LLAVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIII 229
           ++ +A+V    L +T +G+H+ A G N  AAR SGV V RV +  +++SG LAG+ G ++
Sbjct: 183 MVVIAIVISIMLSRTQFGRHIYAVGSNAEAARLSGVKVARVTLWTYVISGTLAGLTGCVL 242

Query: 230 AARLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVS 289
            +RL   QP  G MYEL AIAS VIGGTSL GG G++ G  +G+ +I +L N L +  VS
Sbjct: 243 MSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGTISGTAIGSFVIGILRNGLNMNGVS 302

Query: 290 TYWHNVVIGIVIVVAVTLDILRRR 313
           ++   ++IG+VI++ V +D +R R
Sbjct: 303 SFVQQIIIGLVILLTVWIDQMRNR 326


Lambda     K      H
   0.328    0.143    0.424 

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: 318
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: 317
Length of database: 327
Length adjustment: 28
Effective length of query: 289
Effective length of database: 299
Effective search space:    86411
Effective search space used:    86411
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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