Alignments for a candidate for TM1749 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM1749 in Escherichia coli BW25113

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 14954 b0829 fused predicted peptide transport subunits of ABC superfamily: ATP-binding components (RefSeq)

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__Keio:14954
          Length = 623

 Score =  248 bits (632), Expect = 4e-70
 Identities = 128/266 (48%), Positives = 180/266 (67%), Gaps = 6/266 (2%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63
           +L V NL + F + +  + AV  +S+ L +GE+L IVGESGSGKSV+ L+L+RL+ + G 
Sbjct: 12  VLAVENLNIAFMQDQQKIAAVRNLSFSLQRGETLAIVGESGSGKSVTALALMRLLEQAGG 71

Query: 64  IVDGEAIFLGK------DLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPI 117
           +V  + + L +      +L + N  ++R++RG D+++IFQ PMTSLNP+  VG Q+ E I
Sbjct: 72  LVQCDKMLLQRRSREVIELSEQNAAQMRHVRGADMAMIFQEPMTSLNPVFTVGEQIAESI 131

Query: 118 IWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLI 177
             H+    EEA   A  +L++V IPE+      YP Q SGGMRQRVMIAMAL+C P +LI
Sbjct: 132 RLHQNASREEAMVEAKRMLDQVRIPEAQTILSRYPHQLSGGMRQRVMIAMALSCRPAVLI 191

Query: 178 ADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEA 237
           ADEPTTALDVTIQAQI++L++ L++E  M VIFITHD+ V     DR++ MY G+ VE  
Sbjct: 192 ADEPTTALDVTIQAQILQLIKVLQKEMSMGVIFITHDMGVVAEIADRVLVMYQGEAVETG 251

Query: 238 PVEEILKTPLHPYTKGLLNSTLEIGS 263
            VE+I   P HPYT+ LL +  ++G+
Sbjct: 252 TVEQIFHAPQHPYTRALLAAVPQLGA 277



 Score =  194 bits (493), Expect = 5e-54
 Identities = 111/259 (42%), Positives = 163/259 (62%), Gaps = 14/259 (5%)

Query: 4   LLNVNNLKVEF-------HRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56
           +L V NL   F       +RV   V AV+ +S+ L  GE+L +VGESGSGKS +  +LLR
Sbjct: 313 VLRVRNLVTRFPLRSGLLNRVTREVHAVEKVSFDLWPGETLSLVGESGSGKSTTGRALLR 372

Query: 57  LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116
           L+   G    GE IF G+ +  L+  +L+ +R +DI  IFQ+P  SL+P   +G  ++EP
Sbjct: 373 LVESQG----GEIIFNGQRIDTLSPGKLQALR-RDIQFIFQDPYASLDPRQTIGDSIIEP 427

Query: 117 IIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLL 176
           +  H L+  ++A  R   LLERVG+   P+    YP +FSGG RQR+ IA ALA +PK++
Sbjct: 428 LRVHGLLPGKDAAARVAWLLERVGL--LPEHAWRYPHEFSGGQRQRICIARALALNPKVI 485

Query: 177 IADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236
           IADE  +ALDV+I+ QI+ LL +L+ ++G++ +FI+HD++V      R+  MY G+IVE 
Sbjct: 486 IADEAVSALDVSIRGQIINLLLDLQRDFGIAYLFISHDMAVVERISHRVAVMYLGQIVEI 545

Query: 237 APVEEILKTPLHPYTKGLL 255
            P   + + P HPYT+ LL
Sbjct: 546 GPRRAVFENPQHPYTRKLL 564


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: 470
Number of extensions: 19
Number of successful extensions: 5
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: 623
Length adjustment: 33
Effective length of query: 291
Effective length of database: 590
Effective search space:   171690
Effective search space used:   171690
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources