GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_04059 H281DRAFT_04059 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= uniprot:A0A165KC78
         (242 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04059 H281DRAFT_04059 amino
           acid/amide ABC transporter ATP-binding protein 2, HAAT
           family
          Length = 240

 Score =  325 bits (833), Expect = 5e-94
 Identities = 161/238 (67%), Positives = 201/238 (84%)

Query: 5   SNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDG 64
           + + +L++KGL+V YGGIQAVKG+D EV +GELV+LIG+NGAGKTTTMKAITG      G
Sbjct: 3   TTQAMLKIKGLQVNYGGIQAVKGIDLEVGQGELVTLIGANGAGKTTTMKAITGLKPYAAG 62

Query: 65  NIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEK 124
           +IEY+G+SIKG    +L+K GL MVPEGRG+FARM+I EN+QMGAY+R D  GI AD+++
Sbjct: 63  DIEYMGQSIKGVPPHELLKRGLAMVPEGRGIFARMSIVENMQMGAYLRSDNDGIKADVDR 122

Query: 125 MFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEV 184
           MF  FPRL+ER  Q AGT+SGGEQQMLAM RA++S+PK+LLLDEPSMGLSPIMV+KIFEV
Sbjct: 123 MFGFFPRLKERATQYAGTLSGGEQQMLAMARAIISRPKLLLLDEPSMGLSPIMVEKIFEV 182

Query: 185 VRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242
           VR + A G+T++LVEQNA  AL  A+RGYVM+SGL+TM+G  +Q+L+DPKVRAAYLGE
Sbjct: 183 VRAISAEGMTVLLVEQNARLALQAANRGYVMDSGLVTMSGDAKQMLDDPKVRAAYLGE 240


Lambda     K      H
   0.317    0.136    0.373 

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: 249
Number of extensions: 4
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: 242
Length of database: 240
Length adjustment: 23
Effective length of query: 219
Effective length of database: 217
Effective search space:    47523
Effective search space used:    47523
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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, 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