GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Herbaspirillum seropedicae SmR1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS00870 HSERO_RS00870 ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__HerbieS:HSERO_RS00870
          Length = 378

 Score =  364 bits (935), Expect = e-105
 Identities = 194/369 (52%), Positives = 245/369 (66%), Gaps = 6/369 (1%)

Query: 9   VVAAIAAAAGVASAQE-QVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGK 67
           + A++A     A AQE QVVKIG  +P++G QA  GKDN+ G  MAIE LNAQ +T+GGK
Sbjct: 11  IAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGK 70

Query: 68  KIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGA 127
           KIKF+++AEDD ADPK G A AQKL D  V  +VG  NSG TIPAS+VYND GI   T  
Sbjct: 71  KIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIVVAT-V 129

Query: 128 ATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKK 187
           A+NP +T+ G+ T FR+ A+D+ LG  +A YA   LK K VA+IDDRTAYGQG+A  F K
Sbjct: 130 ASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIK 189

Query: 188 TATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGN 247
            A A G+ VV   FT DKATDF AILT+IK K PDA+F GG  PQGGP+ RQM+QLG+ +
Sbjct: 190 VAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGV-D 248

Query: 248 VKYFGGDGICTSEIAKLAAGAKTLG-NVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQV 306
           V   GGDGIC+ E+ +L  G   +G +V C +GG+ L K   G  +  +Y  KY    + 
Sbjct: 249 VPLMGGDGICSPEMGRL--GGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAET 306

Query: 307 YSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYV 366
           Y+   YD   LI  AMK+ANSVDPK + P LAK S+KGV     F+ N ++K   +T+Y 
Sbjct: 307 YAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYR 366

Query: 367 YKDGKKTPL 375
           +KDG   PL
Sbjct: 367 FKDGLPVPL 375


Lambda     K      H
   0.315    0.131    0.375 

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: 441
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 375
Length of database: 378
Length adjustment: 30
Effective length of query: 345
Effective length of database: 348
Effective search space:   120060
Effective search space used:   120060
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: 42 (22.0 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 (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:

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