GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PfGW456L13_1897 in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385004.1 AMB_RS13205 polyamine ABC
           transporter ATP-binding protein
          Length = 379

 Score =  209 bits (532), Expect = 1e-58
 Identities = 123/301 (40%), Positives = 179/301 (59%), Gaps = 11/301 (3%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           +    ++K +G      +++++L I  GEF  L+G SGCGK+TL+  +AG E  + G IL
Sbjct: 23  IRFEGISKRFGDFT--AVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRIL 80

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           +D  D++ + P +R + M+FQSYAL+P MSV DNIAFGLK   +    I ++VA   +L+
Sbjct: 81  IDGQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELV 140

Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           Q+     RKP QLSGGQ+QRVA+ R LA+ PK+ L DEPL+ LD KLR   + E+  +  
Sbjct: 141 QMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQD 200

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243
           R+  T V VTHDQ EAMT+  ++ VM  G I+Q G+P DIY  P   FVA FIG+   N 
Sbjct: 201 RVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGA--ANM 258

Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQDAG--LEDREVILGIRPEQIILANGE-ANG 300
               ++  +G L           E  L + +AG       V + +RPE++++A  + A+G
Sbjct: 259 FQGSVRGGEGALAIAC----PELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDKPASG 314

Query: 301 L 301
           L
Sbjct: 315 L 315


Lambda     K      H
   0.319    0.138    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: 339
Number of extensions: 14
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: 386
Length of database: 379
Length adjustment: 30
Effective length of query: 356
Effective length of database: 349
Effective search space:   124244
Effective search space used:   124244
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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