GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5403 in Marinobacter adhaerens HP15

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate GFF2245 HP15_2195 amino acid ABC transporter, permease protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>FitnessBrowser__Marino:GFF2245
          Length = 395

 Score =  433 bits (1114), Expect = e-126
 Identities = 218/375 (58%), Positives = 283/375 (75%)

Query: 1   VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEAD 60
           VR+  FQ V +  V   GW L DNT +N++ RGI++GFGFL  +AGFGI  +L+ Y    
Sbjct: 21  VRSLFFQAVAIALVFWGGWILVDNTLSNMESRGISTGFGFLGETAGFGIIMNLVPYDATM 80

Query: 61  SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120
           SY R F +GL NTLLV+ +GV+ ATILGFIIGVARLS NW+++K+A VY+EV RNIP LL
Sbjct: 81  SYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVARLSSNWLVAKMALVYIEVIRNIPLLL 140

Query: 121 QILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVL 180
           QI FWYFAV  ++P PR + + G   F+++RGL +P  +  EGF      ++LAI A+V 
Sbjct: 141 QIFFWYFAVLSNLPSPRQSVDVGGALFLNNRGLYLPDPVTQEGFGIVWGGILLAIAAVVG 200

Query: 181 MTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLI 240
           +  WA KR  ATG+ F  F VG+A+ +++P +S L+ G P+ W++P L+GFNF GG  +I
Sbjct: 201 IRIWAKKRQLATGQIFPTFKVGVAILVLVPIISYLVAGRPLEWDLPALRGFNFGGGITII 260

Query: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 300
           PEL AL +AL++YTA+FIAEIVRSGI SVS GQTEA+++LGL NG TLR V+IPQA+RVI
Sbjct: 261 PELAALWIALSLYTASFIAEIVRSGILSVSKGQTEASKALGLPNGLTLRLVVIPQAMRVI 320

Query: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360
           IPPLTSQYLNL KNSSLA  IGYP++V++F GT LNQTGQA+EV+AITM+VYL IS+ IS
Sbjct: 321 IPPLTSQYLNLVKNSSLATAIGYPDLVAVFMGTTLNQTGQAVEVVAITMAVYLTISLLIS 380

Query: 361 LLMNWYNKRIALIER 375
           L MN YN+ +A+ ER
Sbjct: 381 LFMNIYNRAVAIKER 395


Lambda     K      H
   0.328    0.141    0.430 

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: 500
Number of extensions: 31
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: 375
Length of database: 395
Length adjustment: 30
Effective length of query: 345
Effective length of database: 365
Effective search space:   125925
Effective search space used:   125925
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 (21.8 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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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