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_017220705.1 A923_RS0105740 anaerobic C4-dicarboxylate transporter

Query= TCDB::Q8ZLD2
         (439 letters)



>NCBI__GCF_000276805.1:WP_017220705.1
          Length = 442

 Score =  371 bits (953), Expect = e-107
 Identities = 189/444 (42%), Positives = 299/444 (67%), Gaps = 9/444 (2%)

Query: 1   MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60
           M + E  F+LV L IG+R GG+ LG+V G+G+ + VFIF + P++PP+ V+LIIL+VV  
Sbjct: 1   MLYFEFLFLLVVLYIGSRYGGIGLGVVSGIGLVIEVFIFKMPPTSPPVTVMLIILAVVTC 60

Query: 61  AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120
           A+ L+A+GGL  ++++AE+ILR++P+ +T++APF+ Y  TF+ GTGH VYS++P+I +VA
Sbjct: 61  ASILEAAGGLKYMLQVAERILRKNPKRVTIIAPFVTYAMTFLLGTGHAVYSIMPIIGDVA 120

Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSIS--TIMMICVPATLI 178
             +GIRPERP++ + +ASQ AITASP+SAA+   +  +  +  SI+  +I+M+ VP+TL 
Sbjct: 121 LKNGIRPERPMAAASVASQIAITASPLSAAVVFYLAQLVDIDSSITLLSILMVTVPSTLF 180

Query: 179 GVAMGAIATFNKGKELKDDPEYQRRLAEGL----IKPAQKESKNTVVTSRAKLSVALFLT 234
           G  M A+ +  +GKEL DD EYQ RL + +    I      S +  + ++A+ +V +FL 
Sbjct: 181 GTLMLALYSLRRGKELDDDEEYQARLKDPIWREKILNTTSTSLDEKLPTKARNAVLIFLG 240

Query: 235 SAIVIVLLGLIPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGTV 294
           + + IV++ + P +R + E   G  P+ MS  IQ+ ML+F  +I+L  +     + +G V
Sbjct: 241 AILSIVVIAMFPEIRTITE---GAAPIKMSVVIQMMMLAFGGVILLATKTDPRDVPNGVV 297

Query: 295 FRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQAA 354
           F++G +A +  FG+AWMS+T+    +   +A +  ++  H W  A+ +F VS +V+SQAA
Sbjct: 298 FKSGMVAAIAIFGIAWMSDTYFQYAMPQFRAGIVDMVTLHPWTFALALFIVSVVVNSQAA 357

Query: 355 TTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNHS 414
           T  ++LP+GLALGL    +IG  PAV GYFFIP     +A + FD++GTT+IGKY  NHS
Sbjct: 358 TARMMLPVGLALGLEPALVIGLMPAVYGYFFIPNYPSDIATVNFDNSGTTKIGKYYFNHS 417

Query: 415 FMRPGLVNVIVSVIVGLLIGKMVL 438
           FM  GL+ V+ + +VG ++G++V+
Sbjct: 418 FMAVGLIGVVSACLVGYVLGQIVI 441


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: 385
Number of extensions: 15
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: 439
Length of database: 442
Length adjustment: 32
Effective length of query: 407
Effective length of database: 410
Effective search space:   166870
Effective search space used:   166870
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