GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Marinobacter adhaerens HP15

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit

Query= reanno::psRCH2:GFF857
         (371 letters)



>FitnessBrowser__Marino:GFF960
          Length = 372

 Score =  233 bits (594), Expect = 6e-66
 Identities = 122/297 (41%), Positives = 186/297 (62%), Gaps = 10/297 (3%)

Query: 4   VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63
           +++R I KS+DGT    +++LDI  GE    +G SG GKSTLLR++AG E   +G +++D
Sbjct: 15  LSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLD 74

Query: 64  NQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123
            Q V  LPP  R   M+FQSYAL+PHMTV +N+A GLK   + K EI+ RV A+ +++++
Sbjct: 75  GQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKM 134

Query: 124 DKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRI 183
           +    RKP+ LSGGQ+QRVA+ R++ + PK+ L DEP+  LD  LR +M++E+  + + +
Sbjct: 135 EPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENV 194

Query: 184 RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVE 243
            +T + VTHDQ EAMT+A +I ++  G IAQ+G P+ +Y  P +R  A F+GS  +    
Sbjct: 195 GATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGSVNIFEAH 254

Query: 244 VRAISASPETVTIELPSGYPLTLPV--DGSAVSPGDPLT--LGIRPEH-FVMPDEAD 295
           +R   A   T+T +L     L  PV  D    +P +     + +RPE  ++ PD+ D
Sbjct: 255 IREDEADSVTLTSDL-----LDAPVFIDRGVTTPAESTATLVALRPEKIYLTPDKPD 306


Lambda     K      H
   0.322    0.139    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: 298
Number of extensions: 13
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: 372
Length adjustment: 30
Effective length of query: 341
Effective length of database: 342
Effective search space:   116622
Effective search space used:   116622
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 (21.9 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