GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Synechococcus elongatus PCC 7942

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate Synpcc7942_1379 Synpcc7942_1379 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__SynE:Synpcc7942_1379
          Length = 453

 Score =  456 bits (1174), Expect = e-133
 Identities = 230/451 (50%), Positives = 313/451 (69%), Gaps = 1/451 (0%)

Query: 2   FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYL 61
           F+K+L+ANRGEIA+R++R CEELG+ T+AV+S  D++  HV+ ADEA  IG A ++ SYL
Sbjct: 3   FNKILIANRGEIALRILRTCEELGIGTIAVHSTVDRNALHVQLADEAVCIGEAASSKSYL 62

Query: 62  DHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARS 121
           +  ++I AA   +A AIHPGYGFLAENA FA    D   T++GPS D++  +G+K+ A+ 
Sbjct: 63  NIPNIIAAALTRNASAIHPGYGFLAENARFAEICADHHLTFIGPSPDSIRAMGDKSTAKE 122

Query: 122 LMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQF 181
            MQ   VP +PG+       +    VA + GYPV IKA  GGGGRG+++V    +++  F
Sbjct: 123 TMQRVGVPTIPGSDGLLTDVDSAAKVAAEIGYPVMIKATAGGGGRGMRLVREPADLEKLF 182

Query: 182 ETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEE 241
             A+ E EA F N  +Y+EK+++ PRH+E QILAD +GNV HLGERDCS+QRRHQK++EE
Sbjct: 183 LAAQGEAEAAFGNPGLYLEKFIDRPRHVEFQILADAYGNVVHLGERDCSIQRRHQKLLEE 242

Query: 242 APSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVTE 300
           APSPALS DLR+++G+AA +  +A  Y  AGTVEFLV+  G FYFME+NTRIQVEH VTE
Sbjct: 243 APSPALSADLRQKMGDAAVKVAQAIGYIGAGTVEFLVDATGNFYFMEMNTRIQVEHPVTE 302

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
            +TGLD++  Q+R+A GE L F Q D+++ GH++E RINAE PE  F P  G ++ Y PP
Sbjct: 303 MITGLDLIAEQIRIAQGEALRFRQADIQLRGHAIECRINAEDPEYNFRPNPGRITGYLPP 362

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG G+R+D  V    EI   YDS+I KLIV G+ REE + R +RAL E  I GL T + F
Sbjct: 363 GGPGVRVDSHVYTDYEIPPYYDSLIGKLIVWGATREEAIARMQRALRECAITGLPTTLSF 422

Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEA 451
           H+LML    F  G   T ++++V+ P  +++
Sbjct: 423 HQLMLQMPEFLRGELYTNFVEQVMLPRILKS 453


Lambda     K      H
   0.312    0.132    0.371 

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: 600
Number of extensions: 21
Number of successful extensions: 2
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: 601
Length of database: 453
Length adjustment: 35
Effective length of query: 566
Effective length of database: 418
Effective search space:   236588
Effective search space used:   236588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 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