Alignments for a candidate for mctC in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mctC in Pseudomonas stutzeri RCH2

Align Monocarboxylic acid transporter (characterized)
to candidate GFF2882 Psest_2938 transporter, SSS family

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__psRCH2:GFF2882
          Length = 551

 Score =  426 bits (1094), Expect = e-123
 Identities = 248/557 (44%), Positives = 343/557 (61%), Gaps = 35/557 (6%)

Query: 7   LAQDAVSEGVGNPILN---ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNG 63
           L  DA++  V     N   I +FVVFI  TM +     K  + + D+YT G S +G QNG
Sbjct: 18  LLADAITGEVEKQATNYTAIIMFVVFIAFTMGITKWAAKRNTSTADYYTAGGSITGFQNG 77

Query: 64  LAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADV 123
           LAIAGD++SAASFLGI   +  +GYDG +YSIGF V W + L L+AE LRN+G+FT +DV
Sbjct: 78  LAIAGDFMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILFLMAERLRNLGKFTFSDV 137

Query: 124 LSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVM 183
            S+RL Q  +R+ +A G+L V  FYLIAQM GAG L+ +L  +  +    V V +VG++M
Sbjct: 138 ASYRLGQTQIRLLSAFGSLIVVAFYLIAQMVGAGKLIQLLFGLDYY----VAVVLVGVLM 193

Query: 184 IAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAA 243
           + YVL GGM  TT+VQ+IKAVLL+ G + M ++    V     +L  +AV+ H       
Sbjct: 194 VMYVLFGGMLATTWVQIIKAVLLLSGASFMAIMVMKSVGFDFGSLFAEAVKIH------- 246

Query: 244 TKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSV 303
            KG    QI+ P    G  ++  +  ISL LAL  GTAGLPH+LMRF+TV  AKEARKSV
Sbjct: 247 EKG---AQIMSP----GGLVSDPISAISLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 299

Query: 304 TWAIVLIGAFYLMTLVLGYGAAALVG-----PDRVIAAPGAANAAAPLLAFELGGSIFMA 358
            +A   IG FY++T ++G+GA  LV       D   A  G  N  A  LA  +GG++F+ 
Sbjct: 300 FYATGFIGYFYILTFIIGFGAILLVSTNPEFKDVTGAIVGGTNMVAIHLASAVGGNLFLG 359

Query: 359 LISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISI 418
            ISAVAFAT+LAVVAGL +  ++AV HD+Y  VI+ G++ E +++RV+++T + +G+++I
Sbjct: 360 FISAVAFATILAVVAGLTLAGASAVSHDLYACVIKQGKAREEDEMRVTKLTTLTLGVVAI 419

Query: 419 VLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIF 478
           +LGI+   QN+AF+V LAF++AAS N P +  S+YWK  +T GA+     GL +ALLL  
Sbjct: 420 LLGIIFEKQNIAFMVGLAFSIAASCNFPVLFLSMYWKGLSTRGALFGGSLGLFTALLLTI 479

Query: 479 LSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKP----DNMDDLAAE 534
           +SP V  +    V G   AIFP K P L S+  AF   W  ++  K     +  +   A+
Sbjct: 480 ISPTVWVD----VFGFAEAIFPYKYPALFSMAAAFAGIWFFSVTDKSKRAGEERERFFAQ 535

Query: 535 MEVRSLTGVGVEKAVDH 551
             VRS TG+G   AV H
Sbjct: 536 F-VRSQTGLGATGAVAH 551


Lambda     K      H
   0.324    0.138    0.393 

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: 712
Number of extensions: 41
Number of successful extensions: 6
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: 551
Length of database: 551
Length adjustment: 36
Effective length of query: 515
Effective length of database: 515
Effective search space:   265225
Effective search space used:   265225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. 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 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