GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Azospirillum brasilense Sp245

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 AZOBR_RS21105 AZOBR_RS21105 acetyl-CoA carboxylase

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



>FitnessBrowser__azobra:AZOBR_RS21105
          Length = 666

 Score =  389 bits (999), Expect = e-112
 Identities = 200/447 (44%), Positives = 290/447 (64%), Gaps = 4/447 (0%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           FS++L+ANRGEIA RV++  + +G+  +AVYS+AD+ A+H + ADEA +IG AP+  SYL
Sbjct: 2   FSKILIANRGEIACRVIRTARRLGIKTVAVYSDADRNALHVEMADEAVHIGAAPSAQSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
            I+ I+DA +K    A+HPGYGFLSE  EF EA+  AGI FIGP +  ++ + DK++ K+
Sbjct: 62  LIDRIVDACKKTGAQAVHPGYGFLSEKREFQEALAAAGIAFIGPDAHAIQAMGDKIESKK 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           LA  AGV T PG  G +    EA+ +A  IGYP+M+KA++GGGG G+    N ++  + +
Sbjct: 122 LAKAAGVSTVPGYLGVIADDSEAVTIARDIGYPVMIKASAGGGGKGMRVAWNDEEAREGF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              +  A  +F    +F+EKY   PRHIE Q++ D  G  +   EREC+IQRR+QK+IEE
Sbjct: 182 RSAQNEARSSFADDRVFVEKYIQQPRHIEIQVLADGQGTALYLGERECSIQRRHQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           APSP L    R++M E  +   + ++Y + GT E    D  R+FYFLE+N RLQVEHP T
Sbjct: 242 APSPFLDAATRKAMGEQAVALARAVDYKSAGTVE-FIVDAERNFYFLEMNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           EL+  +DLV+L I++AAGE L   QED++  + G AIE R+ AED   NF  S+G +T+Y
Sbjct: 301 ELVTGLDLVELMIRVAAGEKLTLKQEDIH--LHGWAIESRVYAEDPFRNFLPSTGRLTHY 358

Query: 364 REPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
           R P+  P VRVD+G+  G  +  YYD +++KL  +G +R+ AI     AL  Y I G+  
Sbjct: 359 RPPSEDPHVRVDTGVYEGGEISMYYDPMIAKLCSWGSTRDAAIARMREALDQYYIRGVSH 418

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQK 449
            I     +M +  F EG+ +T++I+++
Sbjct: 419 NIPFLASLMANQRFVEGRLTTNFIAEE 445


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: 750
Number of extensions: 29
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: 666
Length adjustment: 36
Effective length of query: 473
Effective length of database: 630
Effective search space:   297990
Effective search space used:   297990
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: 53 (25.0 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