GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__Pedo557:CA265_RS10520
          Length = 568

 Score =  254 bits (649), Expect = 4e-72
 Identities = 133/254 (52%), Positives = 170/254 (66%), Gaps = 2/254 (0%)

Query: 4   LLNVNNLKVEFHRVEGIV--KAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61
           +LNV +L ++F+  E     KAV  IS+K+ KG  LGIVGESGSGKSV+  S++RL +  
Sbjct: 1   MLNVEHLNIDFYNQEEKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDER 60

Query: 62  GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121
              + GE  F    LL L+  E+R IRG  IS+IFQ PMTSLNP+   G QV E I+ HR
Sbjct: 61  AAKITGEIDFEDISLLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHR 120

Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181
            +   EA++  I L   V +P   K F +YP Q SGG +QRVMIAMAL+C PKLLIADEP
Sbjct: 121 KVDQAEAKKHTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEP 180

Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241
           TTALDVT+Q  I++LL +LK+E  M++IFI+HDL V     D +  MY G+IVE+ P + 
Sbjct: 181 TTALDVTVQKTILQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKS 240

Query: 242 ILKTPLHPYTKGLL 255
           I + P HPYTKGLL
Sbjct: 241 IFENPQHPYTKGLL 254



 Score =  205 bits (521), Expect = 2e-57
 Identities = 109/245 (44%), Positives = 165/245 (67%), Gaps = 8/245 (3%)

Query: 14  FHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73
           F +    VKAVD +++++  GE+LG+VGESG GK+    ++LRLI        GE IF G
Sbjct: 326 FGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTS----GEIIFNG 381

Query: 74  KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNE-EARERA 132
           +++  + K  LR +R KDI IIFQ+P  SLNP + +G  ++EP+  H+L +N+ E +++ 
Sbjct: 382 ENITHIGKTALRKLR-KDIQIIFQDPYASLNPKLSIGQSILEPLQVHKLYRNDSERKQKV 440

Query: 133 IELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQ 192
           +ELL++VG+ E  + F  YP +FSGG RQRV+IA ALA  PK +I DE  +ALDV++QAQ
Sbjct: 441 LELLDKVGLKE--EHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQ 498

Query: 193 IMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTK 252
           ++ L+++L+ E+G++ IFI+HDL+V  +  DRI+ M  GKI EE   E+I   P   YT+
Sbjct: 499 VLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKAAYTQ 558

Query: 253 GLLNS 257
            L+ +
Sbjct: 559 KLIEA 563


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: 475
Number of extensions: 26
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: 324
Length of database: 568
Length adjustment: 32
Effective length of query: 292
Effective length of database: 536
Effective search space:   156512
Effective search space used:   156512
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: 51 (24.3 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