GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847
          Length = 367

 Score =  340 bits (871), Expect = 5e-98
 Identities = 177/358 (49%), Positives = 241/358 (67%), Gaps = 3/358 (0%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  L +K+++K +    +I GIDL++ + EFVVFVGPSGCGKSTLLR+IAGLEE++GG +
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            +DG  + +V P+KR +AMVFQ+YALYPHM+V  NM+F + +A  +K E++++V  AA +
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAARI 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L+L P L+R PK LSGGQRQRVAIGRAI RNPK+FLFDEPLSNLDAALRV  R+E+ +L 
Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           + +   TMIYVTHDQVEAMT+AD++VVL+ G IEQVG+PL+LY +PANLFVA F+G+P M
Sbjct: 181 KEL-QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239

Query: 241 NVIPATIT-ATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299
             +   +T   GQ   V L  G  +TL +       G   + G+RPE L + +  D   +
Sbjct: 240 GFLKGKVTRVNGQSCEVLLDAGTRITLPLSGANLSVGGAVTLGIRPEHLELAQPGDCTLQ 299

Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNG 357
            T  + E LG  T  ++      E +  ++ G      G+ +    D    HLFD +G
Sbjct: 300 VTADVSERLGSDTFCHVL-TSSGEALTMRVRGDLASRYGETLSLHLDAEHCHLFDADG 356


Lambda     K      H
   0.320    0.137    0.387 

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: 382
Number of extensions: 17
Number of successful extensions: 4
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: 362
Length of database: 367
Length adjustment: 29
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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