Aligments for a candidate for TM1746 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for TM1746 in Escherichia coli BW25113

Align TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 15363 b1243 oligopeptide transporter subunit (NCBI)

Query= TCDB::Q9X268
         (642 letters)



>lcl|FitnessBrowser__Keio:15363 b1243 oligopeptide transporter
           subunit (NCBI)
          Length = 543

 Score =  172 bits (435), Expect = 5e-47
 Identities = 115/365 (31%), Positives = 190/365 (52%), Gaps = 17/365 (4%)

Query: 70  PAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEFAWKRAASPETPTLPLWASPVQ 129
           P V ES+  ++D   +TF+LRKD +WS+G PVTA DF ++W+R+  P T +   +AS +Q
Sbjct: 84  PGVAESWD-NKDAKVWTFHLRKDAKWSDGTPVTAQDFVYSWQRSVDPNTASP--YASYLQ 140

Query: 130 Y--IKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSFINMLVLGGAMPLHRKTVQE 187
           Y  I  + +   G KP+ +LGVKA+DD+TL+VTLS P+P F  +LV     P+ +  +++
Sbjct: 141 YGHIAGIDEILEGKKPITDLGVKAIDDHTLEVTLSEPVPYFYKLLVHPSTSPVPKAAIEK 200

Query: 188 HPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFPGNVDRIV---LKAGGLGLQ 244
             E W +P   V NG Y ++ +  N  IVL R+  Y  +    ++++    + +    + 
Sbjct: 201 FGEKWTQPGNIVTNGAYTLKDWVVNERIVLERSPTYWNNAKTVINQVTYLPIASEVTDVN 260

Query: 245 QYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVGYEITRSLSPVFDDIRIRKA 304
           +Y +GEID +   ++   +F    K++  E+H +  +    YEI     P F+D+R+R A
Sbjct: 261 RYRSGEID-MTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQ-KPPFNDVRVRTA 318

Query: 305 LAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIAEAVKGIPYD------PEQAKKLLAEAG 358
           L + +D+ ++ + V     +P + Y  P ++ A+  +   +        E+AKKLLAEAG
Sbjct: 319 LKLGMDRDIIVNKVKAQGNMPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAG 378

Query: 359 YPNGKGFPKVKFYITG-ASDPVAEALVDQWKKVLGITFEIENIESGQFSTLQWSDFVPWA 417
           Y   K       Y T      +A A    WKK +G+  ++ N E   F   +       A
Sbjct: 379 YTADKPLTINLLYNTSDLHKKLAIAASSLWKKNIGVNVKLVNQEWKTFLDTRHQGTFDVA 438

Query: 418 EPGVC 422
             G C
Sbjct: 439 RAGWC 443


Lambda     K      H
   0.319    0.138    0.431 

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: 1003
Number of extensions: 45
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: 642
Length of database: 543
Length adjustment: 37
Effective length of query: 605
Effective length of database: 506
Effective search space:   306130
Effective search space used:   306130
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 (21.7 bits)
S2: 53 (25.0 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:

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 preprint 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

GapMind for catabolism of small carbon sources