GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1746 in Klebsiella michiganensis M5al

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 BWI76_RS17240 BWI76_RS17240 oligopeptide ABC transporter substrate-binding protein OppA

Query= TCDB::Q9X268
         (642 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS17240 BWI76_RS17240 oligopeptide
           ABC transporter substrate-binding protein OppA
          Length = 543

 Score =  182 bits (462), Expect = 3e-50
 Identities = 122/365 (33%), Positives = 196/365 (53%), Gaps = 23/365 (6%)

Query: 49  IFEGLFGYVPDPKSLGGVKVVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEF 108
           +FEGL     D   + GV       E +  ++D   +TF+LRKD +WS+G PVTA DF +
Sbjct: 69  LFEGLLVSDLDGHPVAGV------AEKWD-NKDFKVWTFHLRKDAKWSDGTPVTAQDFVY 121

Query: 109 AWKRAASPETPTLPLWASPVQY--IKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMP 166
           +W+R A P+T +   +AS +QY  + N+ D  +G KP  +LGVKALDD+T +VTLS P+P
Sbjct: 122 SWQRLADPKTASP--YASYLQYGHLANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVP 179

Query: 167 SFINMLVLGGAMPLHRKTVQEHPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGD 226
            F  +LV     P+ +  +++  + W +P   V NG Y ++ +  N  IVL RN  Y  +
Sbjct: 180 YFYKLLVHPSVSPVPKSAIEKFGDKWTQPANIVSNGAYKLKDWVVNERIVLERNTNYWDN 239

Query: 227 FPGNVDRIV---LKAGGLGLQQYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQW 283
               ++++    + +    + +Y +GEID  +     +    LK K++ KE+H +  +  
Sbjct: 240 AKTVINQVTFLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLK-KEIPKEVHVDPYLCT 298

Query: 284 VGYEITRSLSPVFDDIRIRKALAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIAEAVKGI 343
             YEI    +P F D+R+R AL MA+D+ ++ + V     +P ++Y  P ++  + ++  
Sbjct: 299 YYYEINNQKAP-FTDVRVRTALKMALDRDIIVNKVKNQGDLPAYSYTPPYTDGMKLIEPE 357

Query: 344 PYD------PEQAKKLLAEAGYPNGKGFPKVKFYITG-ASDPVAEALVDQWKKVLGITFE 396
            +        E+AKKLLAEAGY   K       Y T      +A A+   WKK LG+  +
Sbjct: 358 WFKWSQEKRNEEAKKLLAEAGYSADKPLTFNLLYNTSDLHKKLAIAVASIWKKNLGVNVK 417

Query: 397 IENIE 401
           +EN E
Sbjct: 418 LENQE 422


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: 1005
Number of extensions: 48
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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:

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 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