GapMind for catabolism of small carbon sources

 

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

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



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

 Score =  393 bits (1009), Expect = e-114
 Identities = 202/359 (56%), Positives = 254/359 (70%), Gaps = 1/359 (0%)

Query: 18  PLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77
           PL+    ++K +    AV+ V L I+KGE F+LLGASGCGK+TLLRMLAGFE P+ G+I+
Sbjct: 21  PLIRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRIL 80

Query: 78  LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137
           +DG D+++VPPY RP+NMMFQSYALFPHM+V  NIAFGLKQD L K  I  +V   L LV
Sbjct: 81  IDGQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELV 140

Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197
            M  F+ RKPHQLSGGQRQRVALAR LAK PK++LLDEP+ ALDKKLR+  QLE+V+I +
Sbjct: 141 QMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQD 200

Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFE 257
           RVG+T VMVTHDQ EAMTM+ RI +MN G   Q+G P +IYE+P TR+ A+FIG+ N+F+
Sbjct: 201 RVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANMFQ 260

Query: 258 GVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAV 317
           G ++   E  L +  P L H L V    +V    PV V +RPEK+M+  + PA+G N+A 
Sbjct: 261 GSVR-GGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDKPASGLNWAE 319

Query: 318 GEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVLT 376
           G V  IAYLGD+S+YHVRL SG+ I A   N H   +   TW D V L W     +VLT
Sbjct: 320 GVVSDIAYLGDVSIYHVRLASGRKIQALRTNLHHGEESRLTWEDPVFLAWHPADSLVLT 378


Lambda     K      H
   0.321    0.137    0.400 

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: 402
Number of extensions: 12
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: 377
Length of database: 379
Length adjustment: 30
Effective length of query: 347
Effective length of database: 349
Effective search space:   121103
Effective search space used:   121103
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: 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