GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas fluorescens FW300-N2C3

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate AO356_00010 AO356_00010 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00010
          Length = 365

 Score =  335 bits (858), Expect = 1e-96
 Identities = 180/356 (50%), Positives = 236/356 (66%), Gaps = 30/356 (8%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M  L++ N+ K F  + ++K I+L V+D EFVVFVGPSGCGKSTLLR+I+GLED T+G I
Sbjct: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            + G+ +T   PAKR +AMVFQ+YALYPH++VR+N++ AL    + K ++  +VAEA+R+
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L L   LDR+P +LSGGQRQRVAIGRA+VR PK+FLFDEPLSNLDAALR+ TRLE++RLH
Sbjct: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           ++L A+MIYVTHDQ+EAMTLA K+VVL  GRIEQ+G+P+ELY++PAN FVA F+G P M 
Sbjct: 181 KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG 240

Query: 241 FVPA--------------------------QRLGGNPGQFIGIRPEYARISPVGPLAGEV 274
           F+ A                            L       IGIRPE+  +   G +    
Sbjct: 241 FLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEGQVLVTT 300

Query: 275 IHVEKLGGDT--NILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAG 328
              E+LG DT  ++ VD GE L  T R+ G  +           D A+C  FDE+G
Sbjct: 301 DVTERLGSDTFCHVNVDSGESL--TVRVQGDCEVPYAARRYLTLDVAHCHLFDESG 354


Lambda     K      H
   0.320    0.137    0.391 

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: 349
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: 331
Length of database: 365
Length adjustment: 29
Effective length of query: 302
Effective length of database: 336
Effective search space:   101472
Effective search space used:   101472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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