GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Marinobacter adhaerens HP15

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 GFF2246 HP15_2196 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein

Query= TCDB::Q52812
         (341 letters)



>FitnessBrowser__Marino:GFF2246
          Length = 347

 Score =  404 bits (1038), Expect = e-117
 Identities = 196/342 (57%), Positives = 248/342 (72%), Gaps = 7/342 (2%)

Query: 4   KLLSAAIGAAVLAVGASAAS----ATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGF 59
           K  S A+G A LAVG  +A+    ATTL +VK KG +QCGV +GL GF+ PD  GNW G 
Sbjct: 9   KTKSIALGIA-LAVGTFSATGAMAATTLENVKEKGHLQCGVTSGLPGFSQPDEKGNWTGI 67

Query: 60  DVDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFR 119
           DVD C+AVA+A+FGD   V++TP  AKERFTALQSGEID+LSRNTTWT+ RD +LG NF 
Sbjct: 68  DVDTCRAVAAAIFGDANAVEFTPLTAKERFTALQSGEIDMLSRNTTWTLTRDASLGLNFA 127

Query: 120 PVTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENL 179
            V YYDGQGF++ KG+ V  A +L GA IC+Q+GTTTELNL+DYF+   +++ P+VF+  
Sbjct: 128 GVNYYDGQGFLINKGIGVDDATQLDGATICIQAGTTTELNLSDYFRAKGMEFKPIVFDTS 187

Query: 180 PEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFD 239
            +    + AGRCDV T+D+S L +LR  L +P    ILP  ISKEPLGP VRQGDDQWF+
Sbjct: 188 EQTVQGFAAGRCDVLTSDRSQLAALRSKLSDPSSAKILPNTISKEPLGPVVRQGDDQWFN 247

Query: 240 IVSWTAYALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVI 299
           IV W  +A INAEE G+T AN D+M  S NP+I+R LG  TD  +G  LGL +D+    +
Sbjct: 248 IVKWVLFAQINAEELGVTSANADDMLKSDNPNIQRLLG--TDGDMGAKLGLPDDFGYQAV 305

Query: 300 KGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341
           K VGNYGE+++RN+G  +PL + RG+NALW +GGI YAPPVR
Sbjct: 306 KLVGNYGEMYDRNVGPDTPLGLDRGINALWTEGGIMYAPPVR 347


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: 407
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: 347
Length adjustment: 29
Effective length of query: 312
Effective length of database: 318
Effective search space:    99216
Effective search space used:    99216
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.

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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