GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisQ in Shewanella sp. ANA-3

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate 7023652 Shewana3_0881 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>lcl|FitnessBrowser__ANA3:7023652 Shewana3_0881 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 226

 Score =  120 bits (302), Expect = 2e-32
 Identities = 70/211 (33%), Positives = 116/211 (54%), Gaps = 12/211 (5%)

Query: 22  LLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLL 81
           L++ G  +T+ ++  ++LL  +LG+     K+SS   +R PA+LY  +IRG P +V+ L+
Sbjct: 23  LILNGLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYIRFPAELYVGVIRGTP-VVVQLV 81

Query: 82  IFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAA 141
           I Y           F+     ++D   A +I  G   GAY +E  R  I +V +GQ EAA
Sbjct: 82  ILY-----------FIVLAAFDVDKVTAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAA 130

Query: 142 TAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKST 201
            + GL +    + ++ PQ ++  LP +GN ++V+LK TA++  IG  DL++A +     T
Sbjct: 131 RSLGLSQAMTMKLIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRAGEIIRSRT 190

Query: 202 YQLFYFLVLAALIYLLITSASNFILRWLERR 232
           ++    L   ALIYL +T +  F+L   E+R
Sbjct: 191 FEDSIPLFTCALIYLFLTYSFTFMLSKFEKR 221


Lambda     K      H
   0.329    0.142    0.418 

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: 129
Number of extensions: 5
Number of successful extensions: 2
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: 242
Length of database: 226
Length adjustment: 23
Effective length of query: 219
Effective length of database: 203
Effective search space:    44457
Effective search space used:    44457
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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