GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889
          Length = 386

 Score =  288 bits (738), Expect = 1e-82
 Identities = 163/370 (44%), Positives = 232/370 (62%), Gaps = 28/370 (7%)

Query: 1   MASVQLQNVTKAWGEVVVS--KDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58
           MA+++L+NV K +G  +    K+I L I +GEF++ VGPSGCGKSTL+  IAGLETIT G
Sbjct: 1   MATLELRNVNKTYGVGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 59  DLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVA 118
            + IG++ ++   P +R + MVFQSYALYP +SV EN+ FGLK+    +  I++ V +VA
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQAAIDEEVTRVA 120

Query: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178
           ++LQ+ HLL+RKP  LSGGQ+QRVA+GR L   P ++L DEPLSNLDA LRV+MR E+  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238
           +H+RL  T +YVTHDQ+EAMTL DK+ V+  G + Q G P ++Y  PA+ FVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240

Query: 239 MNFLPVKV------TATAID--QVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL 290
           MNF+P+++          +D  Q + ELPM  +      +E R+V       LG+RPE +
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQD---AGLEDREV------ILGMRPEQI 291

Query: 291 L-----PSDIADVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAI 345
           +     P+ +  +    EVQV E  G +T + + +   +  +  R    V  + G T  +
Sbjct: 292 MLAGSEPNGLPTI--RAEVQVTEPTGPDTLVFVNLNDTK--VCCRLAPDVAPQPGETLTL 347

Query: 346 GLPPERCHLF 355
              P +  LF
Sbjct: 348 QFDPSKVLLF 357


Lambda     K      H
   0.320    0.137    0.393 

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: 384
Number of extensions: 12
Number of successful extensions: 1
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: 371
Length of database: 386
Length adjustment: 30
Effective length of query: 341
Effective length of database: 356
Effective search space:   121396
Effective search space used:   121396
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: 50 (23.9 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