GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Paucidesulfovibrio gracilis DSM 16080

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 WP_268802025.1 B5D49_RS04650 biotin carboxylase N-terminal domain-containing protein

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



>NCBI__GCF_900167125.1:WP_268802025.1
          Length = 470

 Score =  202 bits (514), Expect = 2e-56
 Identities = 146/449 (32%), Positives = 234/449 (52%), Gaps = 37/449 (8%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           +VL+ANRGEIA R+++A  ++G   +AVY+  D+ + H + A        A  + SY + 
Sbjct: 5   KVLIANRGEIAVRIMEACHDLGHDFVAVYTAEDQASGHVETARTLGGEHCAYRISSYNDA 64

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAV--EKAGITFIGPSSEVMRKIKDKLDGKR 123
             I   A+ A   AIHPGYGF SEN  FA  V   +  + FIGPS  V+R + DK++ KR
Sbjct: 65  GEIFSVADAAQATAIHPGYGFFSENYRFARRVVQRQRPMIFIGPSWWVIRDLGDKINTKR 124

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEK---------IGYPI-MVKAASGGGGVGITRV 173
           LA    VPT PGSD  +    EA ++AE          I  P+ +VKA++GGGG+GI  V
Sbjct: 125 LARSLNVPTVPGSDRAIYDELEAEEIAENLFDFQEAQGISCPVVLVKASAGGGGMGIDEV 184

Query: 174 DNQDQLMDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYG-NYVVAWERECT 232
            + D+   ++ R +  + + F    + IE+   +  H+E Q++ ++ G  +V    R C+
Sbjct: 185 PDMDRFRQIYRRIRNYSMRQFNDEGVLIEQRVFDFNHLEVQIVSERSGQRHVTFGTRNCS 244

Query: 233 IQR-RNQKLIEEAPS----------PALKMEERESMFEPIIKFGKLINYFTLGTFETAFS 281
           +Q    QK IE AP            A K+   + + +  ++  + I Y ++GT+E   +
Sbjct: 245 VQSPGRQKRIETAPGFYPDGITYSFDAQKV--LDDITDYSLRMAEAIKYDSVGTWEWIVT 302

Query: 282 DVSRDFYFLELNKRLQVEHPTTELIFRI------DLVKLQIKLAAGEHLPFSQEDLNKRV 335
               D + LE+N R+QVE+  +  I RI      +L++ QI+LA G+ + +SQ+D+    
Sbjct: 303 P-KGDPFLLEVNTRIQVENGVSAAIARIHGKDGVNLLREQIRLALGDPMGYSQKDIT--F 359

Query: 336 RGTAIEYRINAEDALNNFTGSSGFVTYYREPTGPGVRVDSGI--ESGSYVPPYYDSLVSK 393
            G +IEYRI AED  N F    G +  ++  + P + + + +  +    +P  YD  ++ 
Sbjct: 360 EGVSIEYRIIAEDTTNRFQPWVGQIDTFQWKSAPWLTMHTHVPTDRAYQIPTEYDPNLAL 419

Query: 394 LIVYGESREYAIQAGIRALADYKIGGIKT 422
            IV+G   E A   G+ AL    + G  T
Sbjct: 420 AIVWGADLEEAKARGMVALDGVDLQGNDT 448


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: 507
Number of extensions: 25
Number of successful extensions: 9
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: 470
Length adjustment: 34
Effective length of query: 475
Effective length of database: 436
Effective search space:   207100
Effective search space used:   207100
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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