GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Knoellia flava TL1

Align Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate (characterized)
to candidate WP_035946450.1 N798_RS03995 cation:dicarboxylase symporter family transporter

Query= TCDB::Q1J1H5
         (442 letters)



>NCBI__GCF_000768675.1:WP_035946450.1
          Length = 457

 Score =  395 bits (1015), Expect = e-114
 Identities = 210/410 (51%), Positives = 283/410 (69%), Gaps = 4/410 (0%)

Query: 8   LYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAHMRDTK 67
           LY+ V+IA+VLGI VG + P FG  LK LG  F+ LIKM+I+PIIF T+V GI  +R   
Sbjct: 18  LYIAVIIAMVLGIAVGIIAPDFGVKLKWLGTAFVDLIKMMISPIIFCTIVLGIGSVRRAA 77

Query: 68  KVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQAAGEQS 127
           +VG+VGG AL YF  ++T AL +GL+V NI+KPG G+N+   T + +A  +       ++
Sbjct: 78  QVGKVGGLALGYFLTMSTVALAVGLLVGNIVKPGAGLNL---TDELAASGQKAVGEEHET 134

Query: 128 VADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEAVNSAVFVI 187
             DF+L +IP+TLVSA T G +LQ LL+++L GFAL ++G  G+ +L GI  +   VF +
Sbjct: 135 TVDFILGLIPDTLVSALTAGSVLQTLLVALLVGFALQKMGRAGEPILGGIRHLERLVFRL 194

Query: 188 LGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLG-LIARFAGF 246
           +  +M  APIGAFGAMA  +G  G   L  LA +MVAFY TC LFVFV+LG L+    G 
Sbjct: 195 MAMIMYAAPIGAFGAMAAVVGATGWQALKSLALIMVAFYVTCFLFVFVILGALLKAVTGI 254

Query: 247 SILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSFNLDGTSI 306
           ++   ++++  E LL+L TSSSESALPRLI K+E+AG +R VVG+ VP GYSFNLDGT+I
Sbjct: 255 NVFALLKYLSREFLLILSTSSSESALPRLIAKMEHAGVSRPVVGITVPTGYSFNLDGTAI 314

Query: 307 YLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSAVGHVPVA 366
           YLTMA+LFIA+A +   S+G+Q+ +L  +++ SKGAAGVTG+G  TLA  L +     V 
Sbjct: 315 YLTMASLFIAEALDKPFSIGEQVSLLLFMIIASKGAAGVTGAGLATLAGGLQSHRPDLVD 374

Query: 367 GLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGE 416
           G+  I+GIDR MSEARALTNF GN +AT++I      LD  +L RVL G+
Sbjct: 375 GVGFIVGIDRMMSEARALTNFAGNSIATVLIGHWVGELDRPKLDRVLAGD 424


Lambda     K      H
   0.325    0.142    0.398 

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: 530
Number of extensions: 30
Number of successful extensions: 3
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: 442
Length of database: 457
Length adjustment: 33
Effective length of query: 409
Effective length of database: 424
Effective search space:   173416
Effective search space used:   173416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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