GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Rhodobacter ovatus JA234

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 WP_097031309.1 CRO07_RS14095 acetyl-CoA carboxylase biotin carboxylase subunit

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



>NCBI__GCF_900207575.1:WP_097031309.1
          Length = 448

 Score =  374 bits (960), Expect = e-108
 Identities = 198/445 (44%), Positives = 281/445 (63%), Gaps = 5/445 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F ++L+ANRGEIA RV++A +EMG+ ++AV+S AD  A+H + ADE+  IG A + DSYL
Sbjct: 2   FEKILIANRGEIALRVIRACREMGIKSVAVHSTADADAMHVRMADESVCIGPASSTDSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           +   II A E    +A+HPGYGFLSENA FA+A++  GI FIGP+++ +R + DK+  K 
Sbjct: 62  SKAAIISACEITGAEAVHPGYGFLSENAAFAQALQDHGIEFIGPTADHIRIMGDKITAKE 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
                GVP  PGSDG V   + A+ +A+ IG+P+++KA +GGGG G+    N ++L   +
Sbjct: 122 TMRALGVPCVPGSDGGVPDYEAAIGVAQSIGFPVIIKATAGGGGRGMKVARNAEELEVAF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              +  A  AFG  ++++EKY   PRHIE Q+ GD  G  V   ER+C++QRR+QK+ EE
Sbjct: 182 RTARSEAKAAFGNDEVYMEKYLQRPRHIEIQVFGDGKGRAVHLGERDCSLQRRHQKVFEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           AP P +  E R  +     +    INY   GT E  + D   +FYF+E+N RLQVEHP T
Sbjct: 242 APGPVITPELRAKIGRICAEAVARINYIGAGTIEFLYED--GEFYFIEMNTRLQVEHPVT 299

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E IF +DLV+ QI++AAG  LP S +     + G AIE RINAE  L NFT   G V  +
Sbjct: 300 EAIFGVDLVREQIRVAAG--LPMSLDQEALEINGHAIEVRINAE-KLPNFTPCPGKVRVF 356

Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423
             P G GVR+DS +  G  +PPYYDSL+ KLIV+G  R  A+    RAL +  + G+ TT
Sbjct: 357 HAPGGLGVRMDSALYGGYSIPPYYDSLIGKLIVHGRDRPEALARLHRALGELIVDGVDTT 416

Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448
           + L+  ++ +PD Q G ++  ++ +
Sbjct: 417 VPLFHALLAEPDIQHGDYNIHWLEK 441


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: 559
Number of extensions: 24
Number of successful extensions: 4
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: 448
Length adjustment: 34
Effective length of query: 475
Effective length of database: 414
Effective search space:   196650
Effective search space used:   196650
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 24 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