GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Sinorhizobium meliloti 1021

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate SMc02120 SMc02120 general L-amino acid transport permease ABC transporter protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772
         (223 letters)



>FitnessBrowser__Smeli:SMc02120
          Length = 384

 Score =  116 bits (291), Expect = 5e-31
 Identities = 67/203 (33%), Positives = 109/203 (53%), Gaps = 9/203 (4%)

Query: 15  LWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVITWF 74
           LW G+++TL L  +G+   + LG +LAL R S+  V+  +   ++   R +PL+ V+   
Sbjct: 172 LWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMA 231

Query: 75  YLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134
            + +P  L     +      F   ++   +F +AY  E+VR G+Q+IPKGQ   A +LG+
Sbjct: 232 SVMLPLFLP----QGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGL 287

Query: 135 SYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIGRSNE 194
           S+ Q M  I+LPQA + + P ++   I LF+DTSLV  +G+ D L   R +      +  
Sbjct: 288 SFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATA 347

Query: 195 F-----LIFAGLVYFIISFAASQ 212
                 LIFAG V+++  F  S+
Sbjct: 348 VTPLTGLIFAGFVFWLFCFGMSR 370


Lambda     K      H
   0.332    0.144    0.428 

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: 255
Number of extensions: 11
Number of successful extensions: 1
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: 384
Length adjustment: 26
Effective length of query: 197
Effective length of database: 358
Effective search space:    70526
Effective search space used:    70526
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: 48 (23.1 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:

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