GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_02384 H281DRAFT_02384 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= uniprot:A0A159ZWL6
         (233 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02384 H281DRAFT_02384 amino
           acid/amide ABC transporter ATP-binding protein 2, HAAT
           family
          Length = 254

 Score =  218 bits (555), Expect = 9e-62
 Identities = 113/238 (47%), Positives = 161/238 (67%), Gaps = 6/238 (2%)

Query: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGS--PQAHS-GS 57
           +L    +S  YGK++ALH   ++VR G+IV++IG NGAGKSTLL  + G+     H+ G+
Sbjct: 11  ILDVNGLSVRYGKVEALHGAAIKVRAGQIVSVIGPNGAGKSTLLNAIMGALPTTGHAKGA 70

Query: 58  IRYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKG---DYQEQMD 114
           + Y GE++        + + + +VPE R +FA ++VE+NL +G +   +    ++ +QM+
Sbjct: 71  VVYQGEDVSAVPVEKRVARGMCLVPEKRELFASMSVEDNLVLGAYRRKRAGERNFLDQME 130

Query: 115 KVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFD 174
            V  LFPRLKER  Q  GT+SGGE+QMLA+GRALM KP LL+LDEPSLGLAP+I+++IF 
Sbjct: 131 PVFQLFPRLKERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGLAPLIVKEIFH 190

Query: 175 IIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232
           II  LR+ GV   L+EQNA  AL+I+D  YVLE G + ++G    L  +P+V E YLG
Sbjct: 191 IISALRQTGVATLLIEQNARAALQISDYGYVLETGELALEGAASDLAQNPRVIETYLG 248


Lambda     K      H
   0.320    0.137    0.381 

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: 164
Number of extensions: 7
Number of successful extensions: 3
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: 233
Length of database: 254
Length adjustment: 23
Effective length of query: 210
Effective length of database: 231
Effective search space:    48510
Effective search space used:    48510
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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