GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Acidovorax sp. GW101-3H11

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Ac3H11_694 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_694
          Length = 341

 Score =  224 bits (571), Expect = 2e-63
 Identities = 126/315 (40%), Positives = 191/315 (60%), Gaps = 6/315 (1%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63
           LL + +L+  F      V+AVD +S+ +++GE+LG+VGESGSGKS     L RL++    
Sbjct: 20  LLEIAHLRKHFGSGPHPVRAVDDVSFTIHRGETLGLVGESGSGKSTIGRLLTRLVDPTSG 79

Query: 64  IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123
            +        +DL +L++ + R +R + I IIFQ+P  SLNP +R+   + E +  H L 
Sbjct: 80  QMRYHGGAAPQDLAQLSQSQYRPLRSQ-IQIIFQDPYASLNPRMRIRDVLAEALDTHGLA 138

Query: 124 KNEEARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182
           K      R  +LLE+VG+ PE  +RF   P +FSGG RQR+ IA ALA  P+ ++ADEP 
Sbjct: 139 KGAARLPRIHQLLEQVGLRPEHAERF---PHEFSGGQRQRIGIARALAVEPQFIVADEPL 195

Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242
           +ALDV+IQAQ++ LL ELKE+ G++++FI+HDL V    CDR++ +Y G+++E AP E +
Sbjct: 196 SALDVSIQAQVVNLLGELKEQLGLTLLFISHDLDVVEYLCDRVVVLYLGRVMEIAPTEAL 255

Query: 243 LKTPLHPYTKGLLNST-LEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301
              P HPYT+ LL +  +   ++ + +  + G+ P+P   PSGC F  RC  A   C   
Sbjct: 256 YAQPQHPYTQALLAAAPIPDPAQRRSIALLQGDLPSPANPPSGCVFRTRCPQAEARCASA 315

Query: 302 EPPLVNISENHRVAC 316
           +  L  ++  H  AC
Sbjct: 316 DMQLREVAPGHLHAC 330


Lambda     K      H
   0.320    0.139    0.401 

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: 273
Number of extensions: 13
Number of successful extensions: 4
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: 324
Length of database: 341
Length adjustment: 28
Effective length of query: 296
Effective length of database: 313
Effective search space:    92648
Effective search space used:    92648
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