GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Desulfovibrio vulgaris Hildenborough

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 207710 DVU2226 acetyl-CoA carboxylase, biotin carboxylase, putative

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



>MicrobesOnline__882:207710
          Length = 471

 Score =  195 bits (496), Expect = 3e-54
 Identities = 146/445 (32%), Positives = 228/445 (51%), Gaps = 36/445 (8%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           +VLVANRGEIATR+++A   +G+    VY+  D  + H + A E         + SY + 
Sbjct: 7   KVLVANRGEIATRIVRACHRLGLEFTCVYTAEDAASGHVRLARELGGANSLYRVSSYHDA 66

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAV--EKAGITFIGPSSEVMRKIKDKLDGKR 123
             ++  A+ A   A+HPGYGF +E+  FA  V   +  + FIGPS  V+R++ DK++ KR
Sbjct: 67  NELLAVADDAGCTAVHPGYGFFAEDYRFARRVAQRERKLIFIGPSWRVIRELGDKINTKR 126

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEK---------IGYP-IMVKAASGGGGVGITRV 173
           LA   GVPT PGSD P+    EA K+A+          I  P ++VKA++GGGG+GI  V
Sbjct: 127 LARSLGVPTVPGSDKPIYDELEAEKVAQSLYEFQEQQGIRRPLVLVKASAGGGGMGIEEV 186

Query: 174 DNQDQLMDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYG-NYVVAWERECT 232
            + D    V+ R +  A + F    + IE+   +  H+E Q++ D+ G N V    R C+
Sbjct: 187 YDLDLFKSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQIVSDRTGRNPVHFGTRNCS 246

Query: 233 IQRRN-QKLIEEAPS-PALKME---ERESMFEPI----IKFGKLINYFTLGTFETAFSDV 283
           IQ    QK IE AP      +E   +   +   I    +   + + Y  +GT+E     V
Sbjct: 247 IQSIGLQKRIEVAPGFDPTSIEYGFDAAQVLRDITYHSLAMARKVGYDNVGTWEWI---V 303

Query: 284 SRDF--YFLELNKRLQVEHPTTELIFR-----IDLVKLQIKLAAGEHLPFSQEDLNKRVR 336
           +RD   + +E+N R+QVE+  +  I R     +DL+  QI++  G+ L + QED+     
Sbjct: 304 TRDGHPFLMEVNTRIQVENGVSARIARVNGQEVDLIAEQIRIGLGQPLGYGQEDIT--FE 361

Query: 337 GTAIEYRINAEDALNNFTGSSGFVTYYREPTGPGVRVDSGI--ESGSYVPPYYDSLVSKL 394
           G  IEYR+ AED  N FT   G +  +  P     R+ + +  E    +P  +D  ++  
Sbjct: 362 GVGIEYRLIAEDPDNRFTPWVGRIDAFGWPEEDWARMYTHVPTEEPYDIPTEFDPNLALA 421

Query: 395 IVYGESREYAIQAGIRALADYKIGG 419
           I++G+  E   + G+  L    + G
Sbjct: 422 IIWGKDLEEVKRRGVSFLEGLTLQG 446


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: 532
Number of extensions: 26
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: 509
Length of database: 471
Length adjustment: 34
Effective length of query: 475
Effective length of database: 437
Effective search space:   207575
Effective search space used:   207575
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