GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Bacteroides thetaiotaomicron VPI-5482

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 351443 BT1915 pyruvate carboxylase subunit A (NCBI ptt file)

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Btheta:351443
          Length = 503

 Score =  417 bits (1073), Expect = e-121
 Identities = 224/500 (44%), Positives = 316/500 (63%), Gaps = 13/500 (2%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           ++LVANRGEIA RV+++ +EM +T+IA++SEAD+ A H  YADEAY +G A + +SYLNI
Sbjct: 4   KILVANRGEIAIRVMRSCREMEITSIAIFSEADRTAKHVLYADEAYCVGPAASKESYLNI 63

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
           E II+ A++ H DAIHPGYGFLSENA FA   ++  I FIGP  E M  + DK+  +   
Sbjct: 64  EKIIEVAKECHADAIHPGYGFLSENATFARRCQEENIIFIGPDPETMEAMGDKISARIKM 123

Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185
             AGVP  PG+   + S++EA++L  KIGYP+M+KA+ GGGG G+  + + +++ + +  
Sbjct: 124 IEAGVPVVPGTQENLKSVEEAVELCNKIGYPVMLKASMGGGGKGMRLIHSAEEVEEAYTT 183

Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245
            K  +  +FG   +++EK+   P HIEFQ++GDK+GN +   EREC++QRRNQK++EE P
Sbjct: 184 AKSESLSSFGDDTVYLEKFVEEPHHIEFQILGDKHGNVIHLCERECSVQRRNQKIVEETP 243

Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305
           S  +  E R+ M E  +   K +NY   GT E    D  R++YFLE+N RLQVEHP TE 
Sbjct: 244 SVFVTPELRKDMGEKAVAAAKAVNYIGAGTIE-FLVDKHRNYYFLEMNTRLQVEHPITEE 302

Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365
           +  +DLVK QIK+A G+ L   Q+D+ +  RG AIE RI AED   NF  S G +    E
Sbjct: 303 VVGVDLVKEQIKVADGQVLQLKQKDIQQ--RGHAIECRICAEDTEMNFMPSPGIIKQITE 360

Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425
           P G GVR+DS +  G  +P YYD ++ KLIV+  +REYAI+   R L +YK+ G+K  I 
Sbjct: 361 PNGIGVRIDSYVYEGYEIPIYYDPMIGKLIVWATNREYAIERMRRVLHEYKLTGVKNNIS 420

Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTD---QFVKYLREQEEIKAAIAAEIQSRGLL---RT 479
             + IM  PDF EG + T +I++  +   Q +    E+ E  A IAA +     L   R 
Sbjct: 421 YLRAIMDTPDFVEGHYDTGFITKNGEHLQQCIMRTSERAENIAMIAAYMDYLMNLEENRG 480

Query: 480 SSTDNKGKAQSKSGWKTYGI 499
            +TDN+      S WK +G+
Sbjct: 481 DATDNR----PISKWKEFGL 496


Lambda     K      H
   0.317    0.135    0.385 

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: 637
Number of extensions: 27
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: 509
Length of database: 503
Length adjustment: 34
Effective length of query: 475
Effective length of database: 469
Effective search space:   222775
Effective search space used:   222775
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 (21.6 bits)
S2: 52 (24.6 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