GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Shewanella loihica PV-4

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 5210790 Shew_3218 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)

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



>FitnessBrowser__PV4:5210790
          Length = 1516

 Score =  280 bits (715), Expect = 3e-79
 Identities = 168/456 (36%), Positives = 248/456 (54%), Gaps = 14/456 (3%)

Query: 1    MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYA---DEAYYIGKAP 57
            M P  +VLV  RG  A ++++   +  +  + V S+ D  +V        D+   IG   
Sbjct: 937  MKPIDKVLVHARGCTAVKLIRKAHDNNIKVVLVASDPDMTSVPADMLNENDKLVCIGGNT 996

Query: 58   ALDSYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKD 117
            + +SYLN   ++  AE   VDA+HPG GFLSE+ +FA      G+ F+GPS   M  + +
Sbjct: 997  SDESYLNAYSVLKVAEYEQVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGN 1056

Query: 118  KLDGKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQD 177
            K +  + +    VP  PGS G +T+ ++A+ +A +IGYP+++KA  GGGG GI  V   +
Sbjct: 1057 KSNAIKTSQSQNVPVVPGSHGILTNAEQAVNVANEIGYPVLLKAVQGGGGKGIQVVQRPE 1116

Query: 178  QLMDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRN 237
             ++ ++++    A  AFG  DL++EKY  + RHIE QL+ DK+GN  V   R+C++QR N
Sbjct: 1117 DMISLFQKTSTEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGNTKVLGLRDCSVQRNN 1176

Query: 238  QKLIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQ 297
            QK+IEE+ S  L  E ++ + E     G   +Y   GT E  ++  + + YF+E+N RLQ
Sbjct: 1177 QKVIEESGSTMLPEELKQQVMEYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQ 1236

Query: 298  VEHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTG-- 355
            VEHP TE    ID+V     +AAG     S EDL  +  G AIE R+ AE A  +  G  
Sbjct: 1237 VEHPVTEATSGIDIVSAGFDIAAGR----SIEDLEPQEIGYAIEVRVTAEKAALDSNGVL 1292

Query: 356  ----SSGFVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRA 411
                  G +T    P    + + S    G  V PYYDSL++++I  GESRE  I      
Sbjct: 1293 QLLPHPGMITECVIPERDDIEIISIAGEGKEVSPYYDSLIAQIICRGESREDVINKLHDY 1352

Query: 412  LAD-YKIGGIKTTIELYKWIMQDPDFQEGKFSTSYI 446
            LA+   I GI T I L   I++D  F EG + T+Y+
Sbjct: 1353 LANQVVIKGIATNIPLLTRILKDGTFNEGVYDTNYL 1388


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: 1491
Number of extensions: 69
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: 1516
Length adjustment: 42
Effective length of query: 467
Effective length of database: 1474
Effective search space:   688358
Effective search space used:   688358
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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