GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctA in Halomonas desiderata SP1

Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_176342950.1 BZY95_RS20840 tripartite tricarboxylate transporter permease

Query= TCDB::Q9FA44
         (504 letters)



>NCBI__GCF_002151265.1:WP_176342950.1
          Length = 507

 Score =  425 bits (1092), Expect = e-123
 Identities = 216/502 (43%), Positives = 324/502 (64%), Gaps = 6/502 (1%)

Query: 1   MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60
           MD    L QGFA ++T  N++ AL+G  +G IVG +PGLG + G+A+LLPL F   +   
Sbjct: 1   MDILQSLMQGFATSLTFSNILAALVGAGLGIIVGAIPGLGSVTGIALLLPLTF--QMDPI 58

Query: 61  SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120
           + +I+L  +Y GC YGG  S+ILLN+PGDA A++T+LDGYP++QQG GG AL  + +SSF
Sbjct: 59  TGIIMLGALYYGCMYGGSYSAILLNIPGDAPAVVTSLDGYPLSQQGHGGKALFTANISSF 118

Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180
            G  + I  +    P+LA   L FGPAE  AL++ A+  +G ++  NPLK  ++  IG+ 
Sbjct: 119 IGGTVGIIMLTFMGPILAHVGLMFGPAEVAALILLALCSIGWLLGDNPLKGLISTFIGVM 178

Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHT--SSGQTMVRKT 238
           LAT+G+    G  RFTFDS++L +G+ FI +VIG+F  S++L+M+ +    S + +  + 
Sbjct: 179 LATIGIGTAFGQPRFTFDSMYLLNGISFIPLVIGMFGFSQVLVMMVNRVDPSAKGLSGRL 238

Query: 239 G--RMLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGK 296
           G    L + KE    +  +LRS V+G  VG+LPGAGAT  S ++Y+ EKK+  N D  GK
Sbjct: 239 GLKESLLDRKEALSILPVSLRSGVLGNLVGILPGAGATTGSFLSYVLEKKVGRNGDELGK 298

Query: 297 GDIRGVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDI 356
           G I+GVAA EA NNA+A GSF P+L+LG+PGSGT AV++G L ++ + PGP +F   PD 
Sbjct: 299 GRIQGVAASEAGNNAAAAGSFAPLLSLGIPGSGTAAVLLGGLMMWGLQPGPLLFQNNPDF 358

Query: 357 VWGLIAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLV 416
           VWGLI+++ + NVM ++  + +I    ++L IP   ++P IA V  VG Y+V+++ FD+ 
Sbjct: 359 VWGLISSMYLGNVMAVLAALAIIPFLVKLLLIPASIMIPVIAVVCVVGSYSVNNSMFDVW 418

Query: 417 LMVALGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALL 476
            M+  GV+ + +    +P++PL+L FVL   LE +LR+AL IS G+  I  +S +A  LL
Sbjct: 419 FMLGAGVVAFFMTAARYPIAPLLLAFVLTPRLETSLRQALDISRGDPMIFLRSPIAATLL 478

Query: 477 IMAIMVIVVPPVLRLLRKHSRK 498
            + ++ ++ P   RL     R+
Sbjct: 479 TLILLFVLYPLAKRLFMTVRRR 500


Lambda     K      H
   0.326    0.141    0.414 

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: 788
Number of extensions: 54
Number of successful extensions: 4
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: 504
Length of database: 507
Length adjustment: 34
Effective length of query: 470
Effective length of database: 473
Effective search space:   222310
Effective search space used:   222310
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 (21.6 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