GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Amantichitinum ursilacus IGB-41

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_053937342.1 WG78_RS08300 acetyl-CoA carboxylase biotin carboxylase subunit

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



>NCBI__GCF_001294205.1:WP_053937342.1
          Length = 459

 Score =  398 bits (1023), Expect = e-115
 Identities = 208/447 (46%), Positives = 300/447 (67%), Gaps = 6/447 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+++L+ANRGEIA RVL+A +EMG+  + V+SE D+ A + K ADE+  IG  P+  SYL
Sbjct: 2   FNKILIANRGEIALRVLRACREMGIKTVVVHSEIDREAKYVKLADESVCIGPNPSAQSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           NI  +I AAE    +AIHPGYGFLSENA+FA+ VE++G  FIGP+ E +R + DK+  K 
Sbjct: 62  NIPSLIAAAEVTEAEAIHPGYGFLSENADFAQRVEESGFVFIGPTPESIRLMGDKVSAKN 121

Query: 124 LANMAGVPTAPGSDGPVTSID-EALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182
               AGVP  PGSDG +   D   LKL  ++GYP+++KAA GGGG G+  V  +++L+  
Sbjct: 122 AMKAAGVPCVPGSDGALPDDDASVLKLGREVGYPVIIKAAGGGGGRGMRVVHAEEELLRS 181

Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242
            E  K  A  AFG   +++EK+  NPRHIE Q++ D++G+ +   ER+C++QRR+QK+IE
Sbjct: 182 VEMTKSEAQSAFGNPVVYMEKFLQNPRHIEIQVLADQHGHAIYLGERDCSMQRRHQKVIE 241

Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302
           EAP+P +   +R+ + E   +  + I Y   GTFE  F   + +FYF+E+N R+QVEHP 
Sbjct: 242 EAPAPGITDAQRKRVGEACAEACRKIGYRGAGTFEFLFE--NGEFYFIEMNTRVQVEHPV 299

Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362
           TELI  ID+V+ QI++AAGE L ++Q+D+  +++G A+E RINAED L  F  S G +T 
Sbjct: 300 TELITGIDIVQEQIRVAAGEQLRYTQKDV--KLKGHAMECRINAEDPL-KFVPSPGRITS 356

Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
           Y  P GPGVRVDS +  G +VPP YDS++ K+I YG++RE A+     AL++  + GI T
Sbjct: 357 YHAPGGPGVRVDSHVYQGYFVPPNYDSMIGKIITYGDTREQAMARMRIALSETVVQGIHT 416

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQK 449
            I L++ ++ D +F +G  S  Y+  K
Sbjct: 417 NIPLHQQLLLDAEFIKGGTSIHYLEHK 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: 570
Number of extensions: 26
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: 459
Length adjustment: 34
Effective length of query: 475
Effective length of database: 425
Effective search space:   201875
Effective search space used:   201875
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 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