GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Moritella dasanensis ArB 0140

Align ABC transporter for L-asparagine and L-glutamate, permease subunit 2 (characterized)
to candidate WP_017220928.1 A923_RS0106860 amino acid ABC transporter permease

Query= reanno::pseudo1_N1B4:Pf1N1B4_773
         (223 letters)



>NCBI__GCF_000276805.1:WP_017220928.1
          Length = 359

 Score =  117 bits (294), Expect = 2e-31
 Identities = 64/210 (30%), Positives = 114/210 (54%), Gaps = 8/210 (3%)

Query: 16  WNGMIMTLKLMALGVIGGIILGTILALMRLSHNK-LLSNIAGAYVNYFRSIPLLLVITWF 74
           W G+++T+ + A+G+I    +G +LAL R S N  ++  +   ++ + R +PL+ ++   
Sbjct: 150 WGGLMLTILVAAVGIIASFPIGILLALGRQSDNMPIVKTLCVGFIEFIRGVPLITILFMA 209

Query: 75  YLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134
            + +P        +          ++   +F+AAY  E++R G+Q+IPKGQ  A+++LG+
Sbjct: 210 SVVLPLFF----SDGIEFDKLLRALIGITLFQAAYIAEVIRGGLQAIPKGQYEASESLGL 265

Query: 135 EYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFL---NASRASGDIIGR 191
            Y Q M LIILPQA +   P L+   I LF+DT+LV  +GL D L     + +    +G 
Sbjct: 266 SYWQGMILIILPQALKISIPNLVGSFISLFKDTTLVLIIGLFDILAMVTLTNSDTSWLGF 325

Query: 192 SNEFLIFAGLTYFTISFAASLLVKRLQKRF 221
             E  +F  L Y+   F+ S   + +++R+
Sbjct: 326 EIEGYVFVTLIYWVFCFSMSQYSRVIERRY 355


Lambda     K      H
   0.331    0.144    0.429 

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: 205
Number of extensions: 11
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: 223
Length of database: 359
Length adjustment: 26
Effective length of query: 197
Effective length of database: 333
Effective search space:    65601
Effective search space used:    65601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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:

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