Alignments for a candidate for mctC in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for mctC in Escherichia coli BW25113

Align Monocarboxylic acid transporter (characterized)
to candidate 18095 b4067 acetate permease (NCBI)

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__Keio:18095
          Length = 549

 Score =  439 bits (1128), Expect = e-127
 Identities = 250/558 (44%), Positives = 350/558 (62%), Gaps = 40/558 (7%)

Query: 8   AQDAVSEGVGNPILN---ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGL 64
           A DA+S  V     N   I +F++F++ T+ +     K     +D+YT G + +G QNGL
Sbjct: 18  AADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGL 77

Query: 65  AIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVL 124
           AIAGDY+SAASFLGI   +  +GYDG +YS+GF V W + L L+AE LRN+GR+T ADV 
Sbjct: 78  AIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVA 137

Query: 125 SFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMI 184
           S+RL+Q P+R+ +ACG+L V   YLIAQM GAG L+ +L  ++      + V +VG++M+
Sbjct: 138 SYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN----YHIAVVLVGVLMM 193

Query: 185 AYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAAT 244
            YVL GGM  TT+VQ+IKAVLL+ G + M  +    V      L ++A+  H        
Sbjct: 194 MYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVH-------P 246

Query: 245 KGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVT 304
           KG D   I++P    G  +   +  +SL L L  GTAGLPH+LMRF+TV  A+EARKSV 
Sbjct: 247 KGVD---IMKP----GGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVF 299

Query: 305 WAIVLIGAFYLMTLVLGYGAAALVG--PDRVIAAP---GAANAAAPLLAFELGGSIFMAL 359
           +A   +G FY++T ++G+GA  LVG  P+   AA    G  N AA  LA  +GG++F+  
Sbjct: 300 YATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGF 359

Query: 360 ISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIV 419
           ISAVAFAT+LAVVAGL +  ++AV HD+Y  V + G +TE E++RVS+ITV+++G+I+I+
Sbjct: 360 ISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAII 418

Query: 420 LGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFL 479
           LG+L   QN+AF+V LAFA+AAS N P IL S+YW K  T GA+   + GLI+A++L+ L
Sbjct: 419 LGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMIL 478

Query: 480 SPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME--- 536
            P +       + G + AIFP + P L SI +AF+  W        DN  + A E E   
Sbjct: 479 GPTI----WVQILGHEKAIFPYEYPALFSITVAFLGIW---FFSATDNSAEGARERELFR 531

Query: 537 ---VRSLTGVGVEKAVDH 551
              +RS TG GVE+   H
Sbjct: 532 AQFIRSQTGFGVEQGRAH 549


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: 668
Number of extensions: 30
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: 549
Length adjustment: 36
Effective length of query: 515
Effective length of database: 513
Effective search space:   264195
Effective search space used:   264195
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, or view the source code.

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