GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS10520 CA265_RS10520 ABC
           transporter ATP-binding protein
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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