GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Herbaspirillum seropedicae SmR1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS05965 HSERO_RS05965 ABC transporter ATP-binding protein

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05965 HSERO_RS05965 ABC
           transporter ATP-binding protein
          Length = 404

 Score =  461 bits (1185), Expect = e-134
 Identities = 229/360 (63%), Positives = 282/360 (78%), Gaps = 24/360 (6%)

Query: 15  LLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALM 74
           ++V P + Q FGN+WVRI D+ALLY++LALGLN+VVG+AGLLDLGY+AFYA+GAY   L+
Sbjct: 26  MIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLDLGYIAFYAIGAYSAGLL 85

Query: 75  ASPHLADNFAAFAAMFP----------------NGLHTSLWIVIPVAALLAAFFGAMLGA 118
           ASP  A    +F   +P                NG+H SLW+++P++ALLAA FGA+LGA
Sbjct: 86  ASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLIVPISALLAALFGALLGA 145

Query: 119 PTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDL------ 172
           PTLKLRGDYLAIVTLGFGEIIRIF+NNL+ PVN+TNGP+G+  ID +KVFG+ L      
Sbjct: 146 PTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPIKVFGVSLAGEPGS 205

Query: 173 GKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGIN 232
           G  ++VFG  + SV  YY+LFL+L +  +    RLQDSR+GRAW+AIREDEIAAKAMGIN
Sbjct: 206 GSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQDSRLGRAWVAIREDEIAAKAMGIN 265

Query: 233 TRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVIL 292
           TRN+KLLAF MGASFGGV+GAMFGAFQGFVSPESFSL ES+ ++AMVVLGGIGHIPGV+L
Sbjct: 266 TRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIAVLAMVVLGGIGHIPGVVL 325

Query: 293 GAVLLSALPEVLRYVAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEH 350
           G V+L+ALPEVLR+V  P+Q    G+  +D+ +LRQLL  LAM++IML RP GLWPSP H
Sbjct: 326 GGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGLAMVVIMLTRPAGLWPSPRH 385


Lambda     K      H
   0.328    0.144    0.430 

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: 507
Number of extensions: 18
Number of successful extensions: 5
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: 358
Length of database: 404
Length adjustment: 30
Effective length of query: 328
Effective length of database: 374
Effective search space:   122672
Effective search space used:   122672
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: 50 (23.9 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