GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpT in Pseudomonas fluorescens FW300-N1B4

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Pf1N1B4_593 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= TCDB::G3LHY9
         (356 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_593 Glucose ABC
           transporter, ATP-binding subunit (EC 3.6.3.-)
          Length = 386

 Score =  210 bits (535), Expect = 4e-59
 Identities = 131/362 (36%), Positives = 201/362 (55%), Gaps = 21/362 (5%)

Query: 1   MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60
           MA + L ++   YGA        +LK ++ + NDG    L+GPSGCGK+TL+N I+GL  
Sbjct: 1   MATLELRNVNKTYGAGLPD----TLKNIELKINDGEFLILVGPSGCGKSTLMNCIAGLEN 56

Query: 61  PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120
            S G IL D  D++ +S + R+IA VFQ   +Y TM+V DN+AF L+ R +  A++D  V
Sbjct: 57  ISGGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEV 116

Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180
             + +++ +     RK   L+  Q+Q++++GR L R      LFDEPL+ +D  ++  +R
Sbjct: 117 ARVAKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRP-KIYLFDEPLSNLDAKLRVEMR 175

Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240
           +++K +H++   T VYVTHDQ EA+T  +KV VM DG I Q GTP +++  P++ FV  F
Sbjct: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235

Query: 241 IGSPGMNFMPARIEGSTVKV------GDETLTLEYAPKTSGTAKTE--LGIRPEFIRL-G 291
           IGSP MNF+P R++    ++      G     L    + +G    E  LG+RPE I L G
Sbjct: 236 IGSPPMNFIPLRLQRKDGRLVALLDSGQARCELPLGMQDAGLEDREVILGMRPEQIVLAG 295

Query: 292 RE--GMPITISKV---EDIGRQKIVRARFADQPIAIVVPEDADIPADARVT--FDPSAIS 344
            E  G+P   ++V   E  G   +V     D  +   +  D        +T  FDPS + 
Sbjct: 296 SEPNGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPSKVL 355

Query: 345 IY 346
           ++
Sbjct: 356 LF 357


Lambda     K      H
   0.321    0.137    0.405 

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: 331
Number of extensions: 10
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: 356
Length of database: 386
Length adjustment: 30
Effective length of query: 326
Effective length of database: 356
Effective search space:   116056
Effective search space used:   116056
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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