GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctC in Pseudomonas fluorescens FW300-N1B4

Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate Pf1N1B4_3313 Tricarboxylate transport protein TctC

Query= TCDB::Q9FA46
         (325 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3313
          Length = 325

 Score =  405 bits (1040), Expect = e-118
 Identities = 194/316 (61%), Positives = 248/316 (78%), Gaps = 3/316 (0%)

Query: 9   LTASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVTYMP 68
           L A ++L +  ++A+  P R ECIAPA PGGGFDLTCKL Q +L+    + KPMRVTYMP
Sbjct: 10  LAAGVMLFAGQLMAE--PKRPECIAPASPGGGFDLTCKLAQSALVNEKLLTKPMRVTYMP 67

Query: 69  GGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYGMIA 128
           GGVGAVAYNA+VAQRP + GT+VA+S GSLLNL+QGKFGR+   +VRWLA+VGT YG IA
Sbjct: 68  GGVGAVAYNAVVAQRPADAGTLVAWSSGSLLNLAQGKFGRFDETNVRWLAAVGTSYGAIA 127

Query: 129 VRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYVAFE 188
           V++DSP+KTL DL+ A++KDP+ VVIG+G ++GSQDWM++AL+A+ A ++P  +RYVA E
Sbjct: 128 VKSDSPYKTLDDLVQALKKDPSKVVIGSGGTVGSQDWMQTALIAKAAGINPRDLRYVALE 187

Query: 189 GGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRL-PGQLANIPTAKEQGY 247
           GGGE  TAL+G H+QV S D+S+ +P++    +R+LAVFSE RL   ++ NIPTAKEQGY
Sbjct: 188 GGGEIATALLGGHIQVGSTDISDSMPHIQSGDMRLLAVFSEKRLDEPEMKNIPTAKEQGY 247

Query: 248 DLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTGQQLDDYV 307
           D+VWP++RGFY+GPKVSD DY WW D F KL  +++F K RD R LF F MTG +LD YV
Sbjct: 248 DIVWPVVRGFYLGPKVSDEDYAWWKDAFDKLLASEDFAKLRDQRELFPFAMTGPELDTYV 307

Query: 308 KKQVTDYREQAKAFGL 323
           KKQV DY+  AK FGL
Sbjct: 308 KKQVADYKVLAKEFGL 323


Lambda     K      H
   0.318    0.135    0.401 

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: 407
Number of extensions: 10
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: 325
Length of database: 325
Length adjustment: 28
Effective length of query: 297
Effective length of database: 297
Effective search space:    88209
Effective search space used:    88209
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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