GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Herbaspirillum seropedicae SmR1

Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate HSERO_RS00870 HSERO_RS00870 ABC transporter substrate-binding protein

Query= uniprot:D8IUY1
         (378 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS00870 HSERO_RS00870 ABC
           transporter substrate-binding protein
          Length = 378

 Score =  743 bits (1917), Expect = 0.0
 Identities = 378/378 (100%), Positives = 378/378 (100%)

Query: 1   MFKRVSGLNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERL 60
           MFKRVSGLNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERL
Sbjct: 1   MFKRVSGLNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERL 60

Query: 61  NAQPITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYN 120
           NAQPITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYN
Sbjct: 61  NAQPITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYN 120

Query: 121 DAGIVVATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYG 180
           DAGIVVATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYG
Sbjct: 121 DAGIVVATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYG 180

Query: 181 QGLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKR 240
           QGLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKR
Sbjct: 181 QGLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKR 240

Query: 241 QMKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKY 300
           QMKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKY
Sbjct: 241 QMKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKY 300

Query: 301 NRPAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQS 360
           NRPAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQS
Sbjct: 301 NRPAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQS 360

Query: 361 PVTVYRFKDGLPVPLTSY 378
           PVTVYRFKDGLPVPLTSY
Sbjct: 361 PVTVYRFKDGLPVPLTSY 378


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: 720
Number of extensions: 13
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: 378
Length of database: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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