GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein

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



>FitnessBrowser__pseudo3_N2E3:AO353_25895
          Length = 367

 Score =  394 bits (1013), Expect = e-114
 Identities = 205/358 (57%), Positives = 264/358 (73%), Gaps = 7/358 (1%)

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

Query: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120
            +D   + +V P+KR +AMVFQ+YALYPHM+VR+NM FAL  AGV +AE+EK+VNEAA I
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARI 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 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAA---AGTAVTIGIRPEHFDEA--GPAALD 295
           FLKG +   E Q    L D G  +I + L  A    G AVT+GIRPEH + A  G   L 
Sbjct: 241 FLKGKVTRVERQNCEVLLDAG-TRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCTLQ 299

Query: 296 LAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEG 353
           +  D+ E LG +TF +     +GE + +  +     + G++L+   D     +FD  G
Sbjct: 300 VTADVSERLGSDTFCHVL-TASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDANG 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: 440
Number of extensions: 15
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: 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.

Links

Downloads

Related tools

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