GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  291 bits (746), Expect = 1e-83
 Identities = 161/351 (45%), Positives = 224/351 (63%), Gaps = 7/351 (1%)

Query: 8   DLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNV 67
           +++   G + +L  ++L+I  GEF+V +G SGCGKSTLL  IAGL  +  G + I  R V
Sbjct: 8   NVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRV 67

Query: 68  TWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLL 127
              EP++RG+GMVFQSYALYP M+V  N+SFGLK+AK     + +RV + ++ILQ+  LL
Sbjct: 68  NDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLL 127

Query: 128 KRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTM 187
           +RKP ELSGGQRQRVA+GRA+ R+ D+ LFDEPLSNLDA LR ++R EI RLH  L +TM
Sbjct: 128 QRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTM 187

Query: 188 IYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVE 247
           IYVTHDQ+EA+TLAD+I V+  G ++Q+  P  +Y  P + FVAGF+GSP MNF    ++
Sbjct: 188 IYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQ 247

Query: 248 PKDGRSFVRAGGIAFDVTAYP-AHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDI 306
                S V    + + +T+ P   + L  G  + LG+RPEHV + +A DG  T   VV  
Sbjct: 248 TPGETSLVDT--LVWGITSLPFDSSNLAAGTPLSLGIRPEHVSL-KAADG--TAGVVVTA 302

Query: 307 EEPMGADNLLWL-TFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAE 356
            E +G++  + L T   + +  R      +  G  V L  D+    +FDA+
Sbjct: 303 VEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353


Lambda     K      H
   0.320    0.137    0.392 

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: 386
Number of extensions: 13
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: 361
Length of database: 381
Length adjustment: 30
Effective length of query: 331
Effective length of database: 351
Effective search space:   116181
Effective search space used:   116181
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