GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate GFF137 Psest_0137 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo3_N2E3:AO353_21715
         (220 letters)



>FitnessBrowser__psRCH2:GFF137
          Length = 231

 Score =  133 bits (335), Expect = 2e-36
 Identities = 81/210 (38%), Positives = 118/210 (56%), Gaps = 11/210 (5%)

Query: 17  LLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLI 76
           L+AG  + ++LAL S+A+G V+GLL A A  S + ALR L   Y T++R  P L+ +LLI
Sbjct: 12  LIAGTWMTIQLALASLALGLVLGLLGALAKTSPYSALRWLGGTYSTIVRGVPELLWVLLI 71

Query: 77  YFALPSL-----------GIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGL 125
           YF   S+            + L    +  I L L  GAY TEVFRG LL+IPKG REAGL
Sbjct: 72  YFGTISMIRGIGELFGIENLALSPFAAGTIALGLCFGAYATEVFRGALLAIPKGHREAGL 131

Query: 126 AIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESY 185
           A+GLG+ ++   + +P M R  LP L N F+ L KDT+L + I + E+   ++     S 
Sbjct: 132 ALGLGKRRIFTRLILPQMWRLALPGLGNLFMILMKDTALVSVIGLEEIMRRSQIAVTASK 191

Query: 186 RVIETWLVTTALYVAACYLIAMLLRYLEQR 215
                +LV   +Y+    +  + + +LE+R
Sbjct: 192 EPFTFFLVAAFIYLCLTIVAMVGMHFLEKR 221


Lambda     K      H
   0.329    0.143    0.416 

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: 158
Number of extensions: 8
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: 220
Length of database: 231
Length adjustment: 22
Effective length of query: 198
Effective length of database: 209
Effective search space:    41382
Effective search space used:    41382
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: 46 (22.3 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