GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1747 in Pedobacter sp. GW460-11-11-14-LB5

Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate CA265_RS25300 CA265_RS25300 ABC transporter permease

Query= TCDB::Q9X269
         (341 letters)



>FitnessBrowser__Pedo557:CA265_RS25300
          Length = 351

 Score =  169 bits (428), Expect = 1e-46
 Identities = 114/358 (31%), Positives = 187/358 (52%), Gaps = 55/358 (15%)

Query: 27  FLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGFE 86
           + LK+L+   + M  VI++ +VL  + PG+           AR+T       Q+ L+   
Sbjct: 4   YALKKLMYGLLVMGGVILVVFVLFNILPGD----------PARMTMGQRADVQS-LEAVR 52

Query: 87  ERYGLNNPLWKQILMYL----------------------------KGAVVFKFG--PSFS 116
           + +GL+     Q L+Y+                            K A+V K+    S  
Sbjct: 53  KEFGLDRSKPVQFLLYINDLSPISILDNDSTNQQKYHYAKLMSFDKKALVIKWPYLRSSY 112

Query: 117 DPARNIEDLIKEKFPITFTLALSSILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVA 176
              R++  ++ E  P TF LAL++++FA ++GV LG+L+A+ K++WID TA   +++G++
Sbjct: 113 QTKRDVTAILSETVPNTFILALTAMIFATIIGVFLGVLSAVYKDSWIDKTANAFAILGIS 172

Query: 177 IPSYVVAVFLILIFSIYLG---WLPTSG-------WEG----IRTKILPTIALALGPLAS 222
            PS+   + +  +F   L     L  SG       + G    +R   LP I L L PLA 
Sbjct: 173 APSFFAGIIIAWLFGFVLSNYTGLKMSGSLYSYDPFNGEVLTLRNLWLPMITLGLRPLAI 232

Query: 223 VARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTV 282
           + + TR ++LD L QD+IRTA AKG    T+I KHAL+ +M P++T +    A L+ G+ 
Sbjct: 233 IVQLTRSAMLDVLAQDYIRTARAKGLSRNTIIYKHALKNAMNPVITAISGWFASLLAGSF 292

Query: 283 WVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRIKL 340
           +VE IF   GLG+    A    D+P+++ S   +A   +++N++VD+LYA +DPR+KL
Sbjct: 293 FVEYIFGYNGLGRTTVTALEMSDFPVVMGSILFIAFVFVVINILVDILYAYVDPRVKL 350


Lambda     K      H
   0.328    0.143    0.429 

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: 306
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 341
Length of database: 351
Length adjustment: 29
Effective length of query: 312
Effective length of database: 322
Effective search space:   100464
Effective search space used:   100464
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: 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