Alignments for a candidate for pccA in Thermomonospora curvata DSM 43183

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Thermomonospora curvata DSM 43183

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 WP_012854485.1 TCUR_RS20495 ATP-grasp domain-containing protein

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_000024385.1:WP_012854485.1
          Length = 584

 Score =  525 bits (1352), Expect = e-153
 Identities = 292/599 (48%), Positives = 384/599 (64%), Gaps = 28/599 (4%)

Query: 4   KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63
           KVL+ANRGEIAVR+ RAC + G+ +VAVY+E D    HVR ADEAY +G   AA+SYLD 
Sbjct: 3   KVLIANRGEIAVRIARACRDAGLASVAVYAEPDLDALHVRIADEAYALGGQTAAESYLDI 62

Query: 64  ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123
           E +++ A  + ADA+HPGYGFLAENA+FAR V D+   W+GP  +A+  LG+K KAR + 
Sbjct: 63  EKILKIAADSGADAVHPGYGFLAENADFARAVIDAGLIWIGPPPEAITALGDKVKARHIA 122

Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFET 183
           Q    P+V GT +P    E+V A A+++G P+AIKA  GGGGRGLKV  + +EV   +E+
Sbjct: 123 QKVGAPLVAGTKDPVSGVEEVVAFAEEHGLPIAIKAAYGGGGRGLKVARTLEEVPELYES 182

Query: 184 AKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAP 243
           A RE    F     +VE+YL+ PRH+E Q LAD+HGNV  +  RDCSLQRRHQK++EEAP
Sbjct: 183 AVREAIGAFGRGECFVERYLDKPRHVETQCLADKHGNVVVVSTRDCSLQRRHQKLVEEAP 242

Query: 244 SPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV-EDGEFYFMEVNTRIQVEHTVTEEV 302
           +P L+++  E +  +++  ++ A Y  AGT EFLV +DG   F+EVNTR+QVEH VTEEV
Sbjct: 243 APFLTDEQIELLYSSSKAILKEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPVTEEV 302

Query: 303 TGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGG 362
           TG+D+V+   R+AAGEEL +  DD  + GHS+EFRINAE   + F PA GTL T+ PP G
Sbjct: 303 TGIDLVREMFRIAAGEELGY--DDPPVRGHSIEFRINAEDAGRNFLPAVGTLRTWRPPSG 360

Query: 363 IGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFHR 422
            G+R+D    +G  I   +DS+IAKLIVTG+ RE+ + RA RAL EF ++G  TV+PFHR
Sbjct: 361 PGVRLDSGYEEGQTIPQAFDSLIAKLIVTGATREQAIERARRALAEFTVDGTPTVLPFHR 420

Query: 423 LMLTDEAFREGSHTTKYLDE--VLDPERIEAAVERWSPEAVAGDEEEGEVTER-TFTVEV 479
            +L D A         Y+ E   +    IE   +       A   EE E  ER   TVEV
Sbjct: 421 AVLEDPA---------YVGEPFAVHTRWIETEFDNTIAPYQADPAEESEAAERERITVEV 471

Query: 480 NGKRFEVSLEERGAPAIPLG-GASAAASASKPSGPRKRREESDEGGQQVIEGDGESVAAE 538
            GKR EV+L        P G GAS  A+A K + P +RR     GG       G+S+ + 
Sbjct: 472 GGKRLEVTL--------PAGLGASGGAAAGK-AAPARRRGGRKGGG---ASAGGDSLVSP 519

Query: 539 MQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVL 597
           MQGTI+ V V+EG  V  GDTV +LEAMKME  + A + GTV+ +    GD+V  G V+
Sbjct: 520 MQGTIVKVVVEEGQTVAEGDTVVVLEAMKMEQPLTAHKAGTVTGLSAKVGDTVTNGAVI 578


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: 930
Number of extensions: 48
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 601
Length of database: 584
Length adjustment: 37
Effective length of query: 564
Effective length of database: 547
Effective search space:   308508
Effective search space used:   308508
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources