GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_3374 N515DRAFT_3374 acetyl-CoA carboxylase, biotin carboxylase subunit

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



>FitnessBrowser__Dyella79:N515DRAFT_3374
          Length = 458

 Score =  384 bits (986), Expect = e-111
 Identities = 209/450 (46%), Positives = 290/450 (64%), Gaps = 6/450 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           MP   +V++ANRGEIA RVL+A   +G+  +AV+S AD+   H   ADE+  IG AP++D
Sbjct: 1   MPLLEKVVIANRGEIALRVLRACHSLGIKTVAVHSTADRNLKHVGLADESICIGPAPSVD 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYLNI  II AAE     AIHPGYGFLSE A+FAE VE++G  FIGP+++V+R + DK++
Sbjct: 61  SYLNIPRIIAAAEITDAQAIHPGYGFLSERADFAEQVEQSGFIFIGPTADVIRLMGDKVE 120

Query: 121 GKRLANMAGVPTAPGSDGPV-TSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179
             R    AGVP  PGS GP+   +DE +++A +IGYP+++KAA GGGG G+  V  +  L
Sbjct: 121 AIRAMKAAGVPCVPGSGGPLGDEVDENIRIAREIGYPVIIKAAGGGGGRGMRVVRTEAHL 180

Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239
            +     K+ A  AFG   +++EK+  NPRH+E Q++ D  G+ +   ER+C++QRR+QK
Sbjct: 181 GNAITMTKQEAKAAFGNDQVYMEKFLENPRHVEIQVLADGQGHAIHLGERDCSMQRRHQK 240

Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299
           ++EEAP+P +  E RE + +  +     I Y   GTFE  F   +  FYF+E+N R+QVE
Sbjct: 241 VVEEAPAPGITPELREQIGKVCVDACLRIGYRGAGTFEFLFE--NGRFYFIEMNTRIQVE 298

Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359
           HP TELI  IDLV+ Q+ +A GE L   QED+  ++ G AIE RINAED  ++F  S G 
Sbjct: 299 HPVTELITGIDLVREQLLIAGGEKLSIRQEDI--KIHGHAIECRINAEDP-DSFLPSPGT 355

Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419
           V  +  P GPGVRVD+ +  G  +PP YDS++ KLIV+G  RE AI     ALA+  I G
Sbjct: 356 VKRFEAPGGPGVRVDTHLYDGYKIPPNYDSMIGKLIVHGPDRETAIARMRLALAETVIEG 415

Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQK 449
           +K  I L + IM D  FQ G  +  Y+ ++
Sbjct: 416 VKCNIPLQQRIMADVGFQHGGQNIHYLEKR 445


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: 568
Number of extensions: 26
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: 458
Length adjustment: 34
Effective length of query: 475
Effective length of database: 424
Effective search space:   201400
Effective search space used:   201400
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 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