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.

Links

Downloads

Related tools

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