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_004143816.1 Mesci_4657 cationic amino acid ABC transporter periplasmic binding protein

Query= TCDB::Q52812
         (341 letters)



>NCBI__GCF_000185905.1:YP_004143816.1
          Length = 342

 Score =  531 bits (1368), Expect = e-156
 Identities = 251/334 (75%), Positives = 290/334 (86%), Gaps = 2/334 (0%)

Query: 10  IGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKAVAS 69
           +GAA L + ASAASA TL  VKAKGF+QCGV+TGL GF+APD  G+W G D DFC+AVA+
Sbjct: 9   LGAATLGLMASAASAATLDTVKAKGFIQCGVSTGLAGFSAPDDKGDWQGIDADFCRAVAA 68

Query: 70  AVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDGQGF 129
           AVFGD ++VK+TP +AKERFTALQSGEID+LSRNTTWTINRDTALG NF  VTYYDGQGF
Sbjct: 69  AVFGDGSRVKFTPLSAKERFTALQSGEIDILSRNTTWTINRDTALGLNFIGVTYYDGQGF 128

Query: 130 MV--RKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAYD 187
           M+  +K   V SAL+LSGAA+CVQSGTTTELNLADYFK N ++YNPVVFE L EVNAAYD
Sbjct: 129 MINAKKLPGVNSALQLSGAAVCVQSGTTTELNLADYFKANKMEYNPVVFEKLEEVNAAYD 188

Query: 188 AGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAYA 247
           AGRCDVYTTDQSGLY +RLTL +P +H++LPEIISKEPLGPAVRQGDDQW+ IV WT +A
Sbjct: 189 AGRCDVYTTDQSGLYGIRLTLGSPADHVVLPEIISKEPLGPAVRQGDDQWYHIVKWTYFA 248

Query: 248 LINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNYGE 307
           L+ AEE GIT+ANVDEMKNS +P+IKR LG E DTKIGTDLG++NDW  N++K VGNYGE
Sbjct: 249 LLQAEELGITKANVDEMKNSASPEIKRVLGQEADTKIGTDLGVSNDWVVNIVKAVGNYGE 308

Query: 308 IFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341
           +FERN+G GSPLKIARG+NALW KGG+QYAPP+R
Sbjct: 309 MFERNVGSGSPLKIARGINALWTKGGLQYAPPIR 342


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: 464
Number of extensions: 16
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: 342
Length adjustment: 29
Effective length of query: 312
Effective length of database: 313
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 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