GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Pf6N2E2_807 Various polyols ABC transporter, ATP-binding component

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_807
          Length = 367

 Score =  398 bits (1022), Expect = e-115
 Identities = 204/357 (57%), Positives = 264/357 (73%), Gaps = 5/357 (1%)

Query: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60
           M+ L++ +++K + G  +IKG+DL++   EFVVFVGPSGCGKSTLLR+IAGLEE+S G +
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVSDGTI 60

Query: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120
            +D   + +V P+KR +AMVFQ+YALYPHM+VR+NM FAL  AGVP+AE+EK+VNEAA I
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVPKAEVEKKVNEAARI 120

Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180
           LELG +L+RKPKQLSGGQRQRVAIGRAIVR+PKIFLFDEPLSNLDA LRV MR+E+ARLH
Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180

Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240
           K+L  T++YVTHDQVEAMTLADK+VV+  G +EQVGSPL+LY  PANLFVAGF+G+PKM 
Sbjct: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240

Query: 241 FLKGVIEIDEDQAYARLPDYGD-AKIPVT-LQAAAGTAVTIGIRPEHFD--EAGPAALDL 296
           FLKG +   + Q    L D G    +P +    + G AVT+GIRPEH +  + G   L +
Sbjct: 241 FLKGKVTGLDSQGCEVLLDAGTRINLPRSGANLSVGGAVTLGIRPEHLNLAQPGDCTLQV 300

Query: 297 AIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEG 353
             D+ E LG +TF +     +GE + +  +     + G++L+   D     +FD EG
Sbjct: 301 TADVSERLGSDTFCHV-VTASGEALTMRVRGDLASRFGEQLSLHLDAEHCHLFDAEG 356


Lambda     K      H
   0.321    0.139    0.396 

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: 449
Number of extensions: 17
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: 358
Length of database: 367
Length adjustment: 29
Effective length of query: 329
Effective length of database: 338
Effective search space:   111202
Effective search space used:   111202
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