GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Magnetospirillum magneticum AMB-1

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

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



>NCBI__GCF_000009985.1:WP_011385004.1
          Length = 379

 Score =  245 bits (626), Expect = 1e-69
 Identities = 130/283 (45%), Positives = 178/283 (62%), Gaps = 3/283 (1%)

Query: 4   VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63
           +    I K +       H+DL I  GEF   +G SGCGK+TLLR++AG E  T+G +LID
Sbjct: 23  IRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILID 82

Query: 64  NQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123
            Q V ++PP +R V M+FQSYAL+PHM+VA+N+AFGLK   + K  IK +V A  E++Q+
Sbjct: 83  GQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQM 142

Query: 124 DKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRI 183
            +   RKP  LSGGQRQRVA+ R + +EPKV L DEPL+ LD  LR   ++E+  +  R+
Sbjct: 143 GRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRV 202

Query: 184 RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVE 243
             T + VTHDQ EAMT++ +I V+NAG I QVG P+ +Y YP  RFVA F+G+  M    
Sbjct: 203 GITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANMFQGS 262

Query: 244 VRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPE 286
           VR    +      EL     +T   +  AV+ G P+T+ +RPE
Sbjct: 263 VRGGEGALAIACPELEHDLSVT---EAGAVAAGTPVTVMVRPE 302


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: 317
Number of extensions: 15
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: 371
Length of database: 379
Length adjustment: 30
Effective length of query: 341
Effective length of database: 349
Effective search space:   119009
Effective search space used:   119009
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: 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