GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00885 in Herbaspirillum seropedicae SmR1

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:D8IUY4
         (309 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08275 HSERO_RS08275
           branched-chain amino acid transporter permease subunit
           LivH
          Length = 308

 Score =  243 bits (620), Expect = 4e-69
 Identities = 140/313 (44%), Positives = 203/313 (64%), Gaps = 35/313 (11%)

Query: 6   QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65
           QQ++NGL LG++YALIA+GYTMVYG++ +INFAHG+I M+ + VGL  L  +  V  G P
Sbjct: 10  QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAIG-VQSGYP 68

Query: 66  GIVQLVIAIVGAIPVCIVVSLL----IERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121
               L + + GA+ V ++V+ L    +ER+AYRPLR  PRL PLI+AIG+SI LQ    +
Sbjct: 69  ----LPLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQI 124

Query: 122 IWGRSPLPFPQVMPSDPVHIAGAL-----------ISPTQIMLLALAVLAMVGLVLIVEK 170
             G   +       S PV I+GAL           I  ++++++ + ++ MV L L + +
Sbjct: 125 GQGARDM-------SVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIAR 177

Query: 171 TKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFV 230
           ++MGRA RA AE+  +A L+G+D NKVI  TF +GA LAA+ GV+ A         +GF+
Sbjct: 178 SRMGRACRACAEDMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFI 237

Query: 231 PGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLI 290
            G+KAF+AAVLGGIG+I GAMLGG+LLGL E+  AGY        L S Y+D+ +F +L+
Sbjct: 238 AGIKAFTAAVLGGIGSIPGAMLGGVLLGLAETFAAGY--------LPSEYKDVVSFGLLV 289

Query: 291 IVLTLRPSGIMGE 303
           ++L  RP+G++G+
Sbjct: 290 LILLFRPTGLLGK 302


Lambda     K      H
   0.328    0.144    0.416 

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: 317
Number of extensions: 14
Number of successful extensions: 4
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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 paper from 2022 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