GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Azospirillum brasilense Sp245

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 AZOBR_RS08655 AZOBR_RS08655 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52812
         (341 letters)



>FitnessBrowser__azobra:AZOBR_RS08655
          Length = 340

 Score =  454 bits (1167), Expect = e-132
 Identities = 222/342 (64%), Positives = 260/342 (76%), Gaps = 3/342 (0%)

Query: 1   MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFD 60
           MK+ +L+AA  A V      A +  TL  VK +GFVQCGVN GL GF  PD+SGNW G D
Sbjct: 1   MKSGILAAAAAAVVFGAVTGAQAGPTLDAVKGRGFVQCGVNAGLPGFGNPDSSGNWTGLD 60

Query: 61  VDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRP 120
           VD+C+AVA A+F DP KVK+TP +A++RF A+QSGE+D+LSRNTT T+ RDT++G NF P
Sbjct: 61  VDYCRAVAVALFNDPNKVKFTPLSAQQRFPAIQSGEVDLLSRNTTVTLTRDTSVGLNFAP 120

Query: 121 VTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLP 180
           VTYYDGQGFMV K L VKSA EL+GA +CVQ+GTTTELNLADYF+TNN+ YNPVV E+  
Sbjct: 121 VTYYDGQGFMVNKKLGVKSAKELNGATVCVQAGTTTELNLADYFRTNNMSYNPVVIESND 180

Query: 181 EVNAAYDAGRCDVYTTDQSGLYSLRLTLKN-PDEHIILPEIISKEPLGPAVRQGDDQWFD 239
           EVNAAY AGRCDV TTD SGL   R  +   PD+HIILPEIISKEPL PAVR GDDQWFD
Sbjct: 181 EVNAAYFAGRCDVLTTDASGLAGTRAGVAPVPDDHIILPEIISKEPLAPAVRHGDDQWFD 240

Query: 240 IVSWTAYALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVI 299
           +V WT YA I AEE GIT  NVDE  NS NP+I+R LG  T   +G  LGL   WA N+I
Sbjct: 241 VVKWTVYATIQAEEMGITSKNVDEFVNSKNPEIQRILG--TSPGMGKALGLDEKWAYNII 298

Query: 300 KGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341
           K +GNYGEIFERN+G  +PLK+ RGLNALW  GG+QYA P+R
Sbjct: 299 KTMGNYGEIFERNVGTKTPLKLERGLNALWTNGGLQYAMPIR 340


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: 439
Number of extensions: 21
Number of successful extensions: 3
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: 340
Length adjustment: 28
Effective length of query: 313
Effective length of database: 312
Effective search space:    97656
Effective search space used:    97656
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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