Alignments for a candidate for tctA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for tctA in Pseudomonas stutzeri RCH2

Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate GFF207 Psest_0208 Uncharacterized protein conserved in bacteria

Query= TCDB::Q9FA44
         (504 letters)



>FitnessBrowser__psRCH2:GFF207
          Length = 504

 Score =  694 bits (1792), Expect = 0.0
 Identities = 347/503 (68%), Positives = 416/503 (82%), Gaps = 1/503 (0%)

Query: 1   MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60
           M+T  +L QGF VA  P NL++AL G FVGTIVGLLPGLGPINGVA+LLPLAFAL LP E
Sbjct: 1   METLNFLMQGFDVATRPTNLLVALFGAFVGTIVGLLPGLGPINGVALLLPLAFALGLPPE 60

Query: 61  SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120
           +ALILLA VY+GCEYGGRIS+ILLNVPGDAAA+MT LDGYP+A+QGK G+ALS+SAVSSF
Sbjct: 61  TALILLAAVYLGCEYGGRISAILLNVPGDAAAVMTTLDGYPLARQGKAGIALSLSAVSSF 120

Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180
            GS IA  G++LFAPLLA+W++AFGPAEYF LM+FAIACLG M+   P+K+ +AAL+GL 
Sbjct: 121 VGSTIATCGVVLFAPLLAKWAVAFGPAEYFVLMIFAIACLGGMVGDKPVKTLMAALMGLA 180

Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240
           LATVGVD+ TGVYRFTF SV LSDG+QF++VVIG FSVSEILLMLE T SGQ  V+ +GR
Sbjct: 181 LATVGVDSTTGVYRFTFGSVSLSDGIQFVIVVIGFFSVSEILLMLEKTHSGQKAVKASGR 240

Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300
           +LFN KE      T +RS+V GF +G LPGAGATIASA+TYM+EK+++G+   FG GD+R
Sbjct: 241 LLFNFKEFCLTFWTMVRSAVAGFVIGTLPGAGATIASAMTYMSEKRMAGDKGRFGDGDLR 300

Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360
           G+AAPEAANNASACGS IPMLTLGVPGSGTTAVM+GALTLYNITPGP +F +QPD+VWGL
Sbjct: 301 GLAAPEAANNASACGSLIPMLTLGVPGSGTTAVMIGALTLYNITPGPLLFEQQPDVVWGL 360

Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420
           IA+L I NV+LL+MNIPL+GLF+RML++P W +VP I  +S VGVY+VHST FDLVLMV 
Sbjct: 361 IASLFIGNVILLVMNIPLVGLFSRMLSVPNWVLVPTITVISMVGVYSVHSTVFDLVLMVG 420

Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAI 480
           LGV GY+LRK+ FP+S LILGFVLGEM+E NLRRALSISNG + IL+ S +  AL  + +
Sbjct: 421 LGVFGYLLRKLDFPLSALILGFVLGEMMEDNLRRALSISNGELGILYGSPITLALWALTV 480

Query: 481 MVIVVPPVLRLLRKHSRKPQVDA 503
            ++ +P  LR   K  R   V+A
Sbjct: 481 AMLAMPG-LRWYLKRRRGNVVEA 502


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: 931
Number of extensions: 37
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: 504
Length of database: 504
Length adjustment: 34
Effective length of query: 470
Effective length of database: 470
Effective search space:   220900
Effective search space used:   220900
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources