Aligments for a candidate for aapQ in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments for a candidate for aapQ in Marinobacter adhaerens HP15

Align AapQ, 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 GFF2245 HP15_2195 amino acid ABC transporter, permease protein

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__Marino:GFF2245
          Length = 395

 Score =  380 bits (977), Expect = e-110
 Identities = 202/401 (50%), Positives = 268/401 (66%), Gaps = 7/401 (1%)

Query: 1   MTHEAVDTTPLHGTGWSFRSAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNT 60
           M  + +DT P     W      YDP+ RS+F+Q + I ++    W +  NT  N+     
Sbjct: 1   MKKQTIDTRPAGPKPW------YDPRVRSLFFQAVAIALVFWGGWILVDNTLSNMESRGI 54

Query: 61  ASGFGFLRGRAGFEIGQSLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIG 120
           ++GFGFL   AGF I  +L+ + +  +Y R   VG+ NTLLV+  G+  ATI+GF+IG+ 
Sbjct: 55  STGFGFLGETAGFGIIMNLVPYDATMSYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVA 114

Query: 121 RLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLA 180
           RLS NWL+AK+  VY+EV RNIP LL IFFWY  VLS LP PR+SV +  +++LNNRGL 
Sbjct: 115 RLSSNWLVAKMALVYIEVIRNIPLLLQIFFWYFAVLSNLPSPRQSVDVGGALFLNNRGLY 174

Query: 181 FPKPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVF 240
            P P+   G   V   +++AI A + I  WA KRQ ATGQ F T    +A++V +P++ +
Sbjct: 175 LPDPVTQEGFGIVWGGILLAIAAVVGIRIWAKKRQLATGQIFPTFKVGVAILVLVPIISY 234

Query: 241 VVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQS 300
           +V+G PL +D+P    FN  GG  + PE  +L++ALS YTASFIAEIVR GI  V KGQ+
Sbjct: 235 LVAGRPLEWDLPALRGFNFGGGITIIPELAALWIALSLYTASFIAEIVRSGILSVSKGQT 294

Query: 301 EAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTI 359
           EA+ ALGL      RLVV+PQA+R+IIPPLTSQYLNL KNSSLA AIG+ DLVAV  GT 
Sbjct: 295 EASKALGLPNGLTLRLVVIPQAMRVIIPPLTSQYLNLVKNSSLATAIGYPDLVAVFMGTT 354

Query: 360 LNQSGQAIEIVCIWGIVYLSLSILTSLFMNWFNAKMALVER 400
           LNQ+GQA+E+V I   VYL++S+L SLFMN +N  +A+ ER
Sbjct: 355 LNQTGQAVEVVAITMAVYLTISLLISLFMNIYNRAVAIKER 395


Lambda     K      H
   0.327    0.141    0.432 

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: 576
Number of extensions: 27
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources