GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Klebsiella michiganensis M5al

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 BWI76_RS25540 BWI76_RS25540 acetyl-CoA carboxylase biotin carboxylase subunit

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



>FitnessBrowser__Koxy:BWI76_RS25540
          Length = 449

 Score =  377 bits (969), Expect = e-109
 Identities = 208/445 (46%), Positives = 284/445 (63%), Gaps = 6/445 (1%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           ++++ANRGEIA R+L+A KE+G+  +AV+S AD+   H   ADE   IG AP++ SYLNI
Sbjct: 4   KIVIANRGEIALRILRACKELGIKTVAVHSTADRDLKHVLLADETVCIGPAPSVKSYLNI 63

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
             II AAE     AIHPGYGFLSENA FAE VE++G  FIGP ++ +R + DK+      
Sbjct: 64  PAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKADTIRLMGDKVSAITAM 123

Query: 126 NMAGVPTAPGSDGPV-TSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWE 184
             AGVPT PGSDGP+   +D     A++IGYP+++KA+ GGGG G+  V +  +L     
Sbjct: 124 KKAGVPTVPGSDGPLGEDMDVNRAHAKRIGYPVIIKASGGGGGRGMRVVRSDAELAQSIS 183

Query: 185 RNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEA 244
             K  A  AF    +++EKY  NPRHIE Q++ D  GN +   ER+C++QRR+QK++EEA
Sbjct: 184 MTKAEAKAAFNNDMVYMEKYLENPRHIEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEA 243

Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304
           P+P +  E R  + E   K    I Y   GTFE  F   + +FYF+E+N R+QVEHP TE
Sbjct: 244 PAPGITPELRRYIGERCSKACVDIGYRGAGTFEFLFE--NGEFYFIEMNTRIQVEHPVTE 301

Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364
           +I  +DL+K Q+++AAG+ L   QE++   V+G A+E RINAED  N F  S G +T + 
Sbjct: 302 MITGVDLIKEQLRIAAGQPLSIKQEEV--VVKGHAVECRINAEDP-NTFLPSPGKITRFH 358

Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424
            P G GVR +S I +G  VPPYYDS++ KLI YGE+R+ AI     AL +  I GIKT +
Sbjct: 359 APGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNV 418

Query: 425 ELYKWIMQDPDFQEGKFSTSYISQK 449
           +L   IM D  FQ G  +  Y+ +K
Sbjct: 419 DLQIRIMNDEHFQNGGTNIHYLEKK 443


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: 541
Number of extensions: 21
Number of successful extensions: 5
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: 449
Length adjustment: 34
Effective length of query: 475
Effective length of database: 415
Effective search space:   197125
Effective search space used:   197125
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: 51 (24.3 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