GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Mesorhizobium ciceri WSM1271

Align AapJ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate YP_004141767.1 Mesci_2581 family 3 extracellular solute-binding protein

Query= TCDB::Q52812
         (341 letters)



>NCBI__GCF_000185905.1:YP_004141767.1
          Length = 344

 Score =  273 bits (698), Expect = 5e-78
 Identities = 144/338 (42%), Positives = 200/338 (59%), Gaps = 4/338 (1%)

Query: 1   MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQC-GVNTGLTGFAAPDASGNWAGF 59
           MK    + A+G    A  A AA   TL  VKA+G + C G +    GFA  D  GNW G 
Sbjct: 4   MKWGAAAMALGLVHFAAPAEAAGGKTLEAVKARGVLNCTGHDGSYLGFAEVDDKGNWKGM 63

Query: 60  DVDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFR 119
           D+D C+AVA+AV GDP K+K  P +  +R+ +LQSG++D++ + +  T++RDT LG  F 
Sbjct: 64  DIDLCRAVATAVLGDPAKLKVVPISWAQRWPSLQSGDVDIIIKASGGTLSRDTELGLQFS 123

Query: 120 PVTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENL 179
              Y      M  K LN+KS  + +G  IC+ +GT+ E  +A Y     ++  PV+ E  
Sbjct: 124 MSYYLGTTKVMAHKELNLKSLKDAAGGTICIPAGTSQEQQVAAYTAKLGIKLEPVLIEKT 183

Query: 180 PEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFD 239
            E+  AY +GRCD+Y      L   R+     D+H+ILP++++ EP    +RQGDD W D
Sbjct: 184 EELEQAYFSGRCDLYAQWGPTLAIARIAKSKVDDHVILPDVLAVEPEVMIMRQGDDNWVD 243

Query: 240 IVSWTAYALINAEEFGITQANVDEMKNSP-NPDIKRFLGSETDTKIGTDLGLTNDWAANV 298
           I +WT   LI AE+ GIT  NVDE+K  P +P + +FLG      +G  LGL +DWA  V
Sbjct: 244 IANWTLSTLIFAEQEGITSKNVDEVKAKPTSPQVAKFLG--VTPGMGKGLGLDDDWAYKV 301

Query: 299 IKGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQY 336
           IK VGNYGEIFER++G+ SP K+ R L  LWN GG+ +
Sbjct: 302 IKNVGNYGEIFERDLGKDSPYKMDRELTNLWNNGGVLF 339


Lambda     K      H
   0.316    0.134    0.398 

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: 328
Number of extensions: 13
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: 341
Length of database: 344
Length adjustment: 29
Effective length of query: 312
Effective length of database: 315
Effective search space:    98280
Effective search space used:    98280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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