GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Marinobacter adhaerens HP15

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate GFF4122 HP15_4062 spermidine/putrescine ABC transporter, ATP-binding protein

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__Marino:GFF4122
          Length = 373

 Score =  224 bits (570), Expect = 4e-63
 Identities = 112/255 (43%), Positives = 168/255 (65%), Gaps = 2/255 (0%)

Query: 4   VQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIG 63
           + L N++K +G   V   ++L+I++GEF+  +GPSGCGK+TLLR++AG E    G + + 
Sbjct: 6   LSLSNLSKQFGGKTVLDGLDLEIYDGEFITLLGPSGCGKTTLLRLMAGFEHPDEGTITLA 65

Query: 64  EKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVLQL 123
            + +  T P  R +  VFQ YAL+PH+SV +N+++GLK+    K+ I QRV++   ++QL
Sbjct: 66  GENLTHTAPENRPLNTVFQHYALFPHMSVFDNVAYGLKMEKRPKDEIRQRVDEALAMVQL 125

Query: 124 AHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRL 183
                RKP  LSGGQ+QRVAI R +V  P + LLDEPLS LD  LR  M++E+ RL + L
Sbjct: 126 QDFARRKPHQLSGGQQQRVAIARAVVKRPRLLLLDEPLSALDYKLRRTMQVELKRLQREL 185

Query: 184 GRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFLP 243
           G T ++VTHDQ EA++++D++VVL  G V Q+G P E+Y  PA+ F A F+G  + NF P
Sbjct: 186 GITFVFVTHDQEEALSMSDRVVVLKDGLVQQLGTPREVYERPANLFTARFVG--ETNFFP 243

Query: 244 VKVTATAIDQVQVEL 258
             V +     ++V++
Sbjct: 244 GTVESVQDGSIKVDV 258


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: 334
Number of extensions: 10
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: 373
Length adjustment: 30
Effective length of query: 341
Effective length of database: 343
Effective search space:   116963
Effective search space used:   116963
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