GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yhiT in Moritella dasanensis ArB 0140

Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate WP_017220126.1 A923_RS0102800 anaerobic C4-dicarboxylate transporter

Query= TCDB::Q8ZLD2
         (439 letters)



>NCBI__GCF_000276805.1:WP_017220126.1
          Length = 433

 Score =  357 bits (915), Expect = e-103
 Identities = 189/441 (42%), Positives = 275/441 (62%), Gaps = 11/441 (2%)

Query: 1   MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60
           M   +L  +L+ + +GARIGG+ +G  GG GV V+  I GL   + PIDVILII+SV+ A
Sbjct: 1   MIVVQLFVVLLFIYLGARIGGIGIGFAGGAGVLVLTMILGLDAGSIPIDVILIIMSVITA 60

Query: 61  AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120
            A++Q +GG+D LV LAEK LR++P+ IT  AP + Y  T ++GTGH  +S LPVI+EVA
Sbjct: 61  IAAMQVAGGMDWLVDLAEKFLRKNPKRITFYAPIVTYFMTVLAGTGHTAFSTLPVIAEVA 120

Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSISTIMMICVPATLIGV 180
           ++ GIRP RPLSI+V+ASQ AITASPISAA+    G++ PLGV   +++ +C+P+T +  
Sbjct: 121 KEQGIRPSRPLSIAVVASQIAITASPISAAVVFFSGILEPLGVDYLSLLAVCIPSTFLAC 180

Query: 181 AMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAKLSVALFLTSAIVIV 240
            +GA      G ELKDDP YQ RLA+GLIK   +  ++ + T  AK SV +F  + + +V
Sbjct: 181 MVGAFVANYLGCELKDDPVYQDRLAKGLIKMNGEGKRDILPT--AKTSVYIFCAAIVAVV 238

Query: 241 LLGLIPALRPMVETAKGL---QPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGTVFRA 297
                 A   M+  + GL     +  + AI   ML+ A  IV   +    QI +   F++
Sbjct: 239 ------AYATMISGSVGLIENPTIGRNEAIMALMLTAAACIVSFTKIDASQIANAATFKS 292

Query: 298 GALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQAATTL 357
           G  A VC  G+AW+ +TFV+ HI  IK    ++L+Q+ W++A+++FF S ++ SQ ATT 
Sbjct: 293 GMSACVCVLGVAWLGDTFVSAHIGDIKEFSASILEQYPWMLAVVLFFASMLLYSQGATTT 352

Query: 358 ILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNHSFMR 417
            L+P  LA+G+     + S+ AV+  F +P     LAA+  DDTG+TRIG  V NH F  
Sbjct: 353 ALMPAALAIGVAPITAVASFAAVSALFVLPTYPTLLAAVEMDDTGSTRIGNLVFNHPFFI 412

Query: 418 PGLVNVIVSVIVGLLIGKMVL 438
           PG+  +  SV +G + G ++L
Sbjct: 413 PGVATISTSVALGFVFGGLIL 433


Lambda     K      H
   0.328    0.141    0.409 

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: 391
Number of extensions: 13
Number of successful extensions: 2
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: 439
Length of database: 433
Length adjustment: 32
Effective length of query: 407
Effective length of database: 401
Effective search space:   163207
Effective search space used:   163207
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 (21.8 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