GapMind for catabolism of small carbon sources

 

Alignments for a candidate for N515DRAFT_2924 in Methylocystis bryophila S285

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>NCBI__GCF_002117405.1:WP_102938052.1
          Length = 481

 Score =  447 bits (1150), Expect = e-130
 Identities = 226/462 (48%), Positives = 311/462 (67%), Gaps = 9/462 (1%)

Query: 26  EATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCY 85
           E  LKRAL    L+ +GIG IIGAGIFV+TGQAAA++AGP + +SF+ +G+AC   ALCY
Sbjct: 26  ENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLACTFVALCY 85

Query: 86  AEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALIS 145
           AE AA++P +GS Y+Y+Y TLGE  AW +GW+LVLEY    ATVA GW+GYFN+++    
Sbjct: 86  AELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFNRVMQ--- 142

Query: 146 GWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSI 205
              G  + LP+ L +A F          G+F N+PA AII  +T L   G ++S+F N+I
Sbjct: 143 ---GLGIHLPEALTSAYFANAHSIGGTHGVF-NVPAAAIILLLTALLMRGTSESSFFNNI 198

Query: 206 IVAIKVTVILLFIAFATKYINPDNWHPFIPA-SEGASKYGWAGVGRAAAIVFFSYIGFDA 264
           IV IKV V+L+ I     +++  NW P IP  ++    +GW+GV R A++VFF+YIGFD 
Sbjct: 199 IVVIKVMVVLVVIFVGAAHVDAANWTPLIPENTDHFGHFGWSGVVRGASVVFFAYIGFDG 258

Query: 265 VSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYP 324
           VSTAA EA  PQRD+PIGI+GSL++CTILY+ VA + TG+  ++ LG P+P++  +D   
Sbjct: 259 VSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYKELGVPDPMALVMDR-T 317

Query: 325 SLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTV 384
            + WL  +V +GA+ GL++ +L++L GQ RIFY+MA+DGL+P VF  +H  +RTP V   
Sbjct: 318 GVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVFAAVHPVWRTPAVSQA 377

Query: 385 VVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVC 444
           +VGV  A   GLF I +L EMV++GTL AFA VC  VL LR ++P++ R FR P    + 
Sbjct: 378 LVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLRRSQPDMHRPFRAPGIPAMP 437

Query: 445 PLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSK 486
            LG  +C+AL +   LE W  ++ W AIG AIYF YG  H+K
Sbjct: 438 LLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFYGVKHAK 479


Lambda     K      H
   0.328    0.141    0.441 

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: 745
Number of extensions: 44
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: 492
Length of database: 481
Length adjustment: 34
Effective length of query: 458
Effective length of database: 447
Effective search space:   204726
Effective search space used:   204726
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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