GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Sinorhizobium meliloti 1021

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 SMc01345 SMc01345 acetyl-CoA carboxylase biotin carboxylase subunit

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



>lcl|FitnessBrowser__Smeli:SMc01345 SMc01345 acetyl-CoA carboxylase
           biotin carboxylase subunit
          Length = 449

 Score =  375 bits (962), Expect = e-108
 Identities = 201/446 (45%), Positives = 287/446 (64%), Gaps = 6/446 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           M   S++L+ANRGEIA RVL+A KE+G+  +AV+S AD  A+H + ADE+  IG  P+ +
Sbjct: 1   MAMISKILIANRGEIALRVLRACKELGIATVAVHSTADSDAMHVRLADESVCIGPPPSRE 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYLNI  I+ A E    DA+HPGYGFLSENA+FA+ ++  GITFIGP++E +R + DK+ 
Sbjct: 61  SYLNIHQIVAACEITGADAVHPGYGFLSENAKFADILDAHGITFIGPTAEHIRLMGDKIT 120

Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180
            K+ A   G+P  PGSDG V   + AL++A +IG+P+++KA +GGGG G+     +++L 
Sbjct: 121 AKKTAEELGIPVVPGSDGEVRP-ENALEIARQIGFPVLIKATAGGGGRGMKVARTEEELE 179

Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240
           +     +  A  AFG   +++EK+   PRHIE Q++GD  GN +   ER+C++QRR+QK+
Sbjct: 180 NAVATARSEAAAAFGNDAVYMEKFLGKPRHIEIQVVGDGEGNAIHLGERDCSLQRRHQKV 239

Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300
            EEA SPAL +E+R  + +      K + Y   GT E  +   + +FYF+E+N RLQVEH
Sbjct: 240 WEEANSPALNVEQRMKIGQVCADAMKKLKYRGAGTIEFLYE--NGEFYFIEMNTRLQVEH 297

Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360
           P TE I  IDLV  QI++A+G  L   QED+     G AIE RINAED    F  S G +
Sbjct: 298 PITEAITGIDLVHEQIRVASGAGLSAKQEDI--VFSGHAIECRINAEDP-RTFVPSPGTI 354

Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420
           T++  P G GVRVDSG   G  +PPYYDSL+ KLIV+G +R   +    R L ++ I GI
Sbjct: 355 THFHAPGGLGVRVDSGAYQGYRIPPYYDSLIGKLIVHGRTRVECMMRLRRVLDEFVIDGI 414

Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYI 446
           KTT+ L++ ++ + D   G +   ++
Sbjct: 415 KTTLPLFQDLINNQDIANGDYDIHWL 440


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: 557
Number of extensions: 24
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: 449
Length adjustment: 34
Effective length of query: 475
Effective length of database: 415
Effective search space:   197125
Effective search space used:   197125
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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