GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Caulobacter crescentus NA1000

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 CCNA_02261 CCNA_02261 propionyl-CoA carboxylase biotin-containing subunit

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



>FitnessBrowser__Caulo:CCNA_02261
          Length = 669

 Score =  358 bits (918), Expect = e-103
 Identities = 205/503 (40%), Positives = 293/503 (58%), Gaps = 15/503 (2%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           FS++L+ANRGEIA RV+K  + +G+  + VYS+AD  ++  + ADE  +IG +PA  SYL
Sbjct: 2   FSKILIANRGEIAVRVIKTCRRLGIKTVVVYSDADAGSLAVEMADETVHIGASPANQSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
             + II A ++    A+HPG+GFLSENA FA+     GI FIGP+   +  + DK++ K+
Sbjct: 62  VADKIIAACKQTGAQAVHPGFGFLSENAGFAQRCADEGIVFIGPNPGAISAMGDKIESKK 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
            A  AGV   PG  G +    EA+K++E+IGYP+M+KA++GGGG GI     +  + + +
Sbjct: 122 FAQAAGVSCVPGHIGEIADTAEAVKISEEIGYPVMIKASAGGGGKGIRVAWTRKDVEEGF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              +  A  +FG   +FIEK+  +PRHIE Q++GDK+GN V  +EREC+IQRRNQK+IEE
Sbjct: 182 PAVRAEAKASFGDDRIFIEKFIESPRHIEIQVLGDKHGNVVHLFERECSIQRRNQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           APSP L    R +M    +   K +NY + GT E   +   + F+FLE+N RLQVEHP T
Sbjct: 242 APSPLLDEATRNAMGAQAVALAKAVNYDSAGTVEFV-AGQDKSFFFLEMNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           ELI  +DLV+  I+ A GE + F Q DL+  + G AIE RI AED    F  S G +  Y
Sbjct: 301 ELITGLDLVEQMIRSAYGEKMAFGQSDLS--INGWAIESRIYAEDPYRKFLPSIGRLVRY 358

Query: 364 REPT-----GPG----VRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALAD 414
             P      GP     VR D+G+  G  +  +YD ++SKL  +  +R  AI    RAL D
Sbjct: 359 DPPAEGDKDGPNGGYVVRNDAGVREGDEISMFYDPMISKLCTWAPTRLAAIDGMGRALED 418

Query: 415 YKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQK-TDQF--VKYLREQEEIKAAIAAEI 471
           + I G+   I     +M +  F+ GK +TSYI  +  D F        Q +I  A+ A +
Sbjct: 419 FHIEGLGQNIPFLAAVMDEERFRSGKLATSYIKDEFPDGFNGTTPTAVQLDILTAVGAAM 478

Query: 472 QSRGLLRTSSTDNKGKAQSKSGW 494
           Q     R  S ++    +++  W
Sbjct: 479 QRVYATRARSYESGLIGEARDEW 501


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: 770
Number of extensions: 30
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: 669
Length adjustment: 36
Effective length of query: 473
Effective length of database: 633
Effective search space:   299409
Effective search space used:   299409
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