GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate AO353_03840 AO353_03840 ABC transporter ATP-binding protein

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03840
          Length = 351

 Score =  264 bits (674), Expect = 3e-75
 Identities = 154/357 (43%), Positives = 216/357 (60%), Gaps = 12/357 (3%)

Query: 1   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60
           M  + L+NV K +G     KD+NL + EG+ V F+GPSGCGK+TLLRMIAGLET++ G++
Sbjct: 1   MTGLILENVEKRYGTACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60

Query: 61  FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120
            + ++ + +TP   R  GMVFQS AL+PH++V EN+++ LKL G  K     RV ++ E+
Sbjct: 61  RLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELLEL 120

Query: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180
           +QL  ++DR    LSGGQRQRVAI R + + P + LLDEPLS LDA LR  M++EI +L 
Sbjct: 121 IQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240
           +RL  T I VTHDQ EAMT+AD +VVL   RV QVG P+E+Y +PA+ FVA FIGS   N
Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGQNRVQQVGTPIEIYRHPANEFVADFIGSG--N 238

Query: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLL---PSDIAD 297
             P    ATA+   +V LP  +  QV  P+ S  + VG  + + +RPE L    P   A 
Sbjct: 239 IFP----ATALGDGKVGLPGGDALQV--PICS-SIVVGEKVKMLVRPEDLQLSHPQATAG 291

Query: 298 VILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHL 354
             L G V  V  +G   +  ++   +    +      + +  G   ++ +P E C +
Sbjct: 292 NRLLGRVTFVRDIGATIETTVECSGVTLTALSTPCQGIGLSIGNPVSVTIPSEACRV 348


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: 337
Number of extensions: 15
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: 351
Length adjustment: 29
Effective length of query: 342
Effective length of database: 322
Effective search space:   110124
Effective search space used:   110124
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