GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Burkholderia phytofirmans PsJN

Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate BPHYT_RS19350 BPHYT_RS19350 amino acid ABC transporter substrate-binding protein

Query= uniprot:D8IUY1
         (378 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS19350 BPHYT_RS19350 amino acid
           ABC transporter substrate-binding protein
          Length = 382

 Score =  320 bits (819), Expect = 5e-92
 Identities = 166/370 (44%), Positives = 241/370 (65%), Gaps = 6/370 (1%)

Query: 3   KRVSGLNIIAA-SLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLN 61
           K+++G  ++AA SLA     A AQ T+ VK+GF+ P+TG QA  GKD Q G+ +A+E +N
Sbjct: 6   KQLAGAALVAAMSLA---GTANAQSTEDVKVGFAGPMTGAQAHYGKDFQNGITLAVEDMN 62

Query: 62  AQPITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYND 121
           A    +GGK+++F + + DDQADP++G  VAQKL D G+K ++G +NSG TIPASR+Y +
Sbjct: 63  ATKPVIGGKQVRFVLDSADDQADPRTGTTVAQKLVDDGIKGMLGHFNSGTTIPASRIYAN 122

Query: 122 AGIVVATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQ 181
           AGI    +A+ P+ TQQGF T FR+  SD+Q G     +A K L  K++A++DDRTAYGQ
Sbjct: 123 AGIPEIAMATAPEYTQQGFKTTFRMMTSDTQQGSVAGTFAVKTLGVKKIAIVDDRTAYGQ 182

Query: 182 GLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQ 241
           GLA +F K AKA G  +V  ++TNDKA DF +ILT +K  +PD ++ GG   Q  P+ +Q
Sbjct: 183 GLADQFEKAAKAAGGQIVDREYTNDKAVDFKSILTKLKSVQPDLIYYGGADSQAAPMVKQ 242

Query: 242 MKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYN 301
           MK LG+  PLMGG+ + +P   ++ GDA   +V  +  G  L++   GK +  +Y+K++N
Sbjct: 243 MKALGIKAPLMGGEMVHTPTFIQIAGDAANGTV-ASLAGLPLEEMPGGKDYVAKYKKRFN 301

Query: 302 RPAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGV-AGQYDFDANHDLKQS 360
              +TY+   YDG M +  AMK+ANS DP ++ P LAK S   V +    +D+  DLK  
Sbjct: 302 EDVQTYSPYAYDGAMAMFDAMKKANSTDPAKYLPVLAKTSMPAVTSANLAYDSKGDLKNG 361

Query: 361 PVTVYRFKDG 370
            +T+Y+  DG
Sbjct: 362 GITLYKVVDG 371


Lambda     K      H
   0.316    0.134    0.378 

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: 465
Number of extensions: 20
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: 378
Length of database: 382
Length adjustment: 30
Effective length of query: 348
Effective length of database: 352
Effective search space:   122496
Effective search space used:   122496
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 (21.6 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, 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