Aligments for a candidate for mcmA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Caulobacter crescentus NA1000

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate CCNA_02459 CCNA_02459 methylmalonyl-CoA mutase alpha subunit

Query= BRENDA::Q84FZ1
         (721 letters)



>FitnessBrowser__Caulo:CCNA_02459
          Length = 714

 Score = 1070 bits (2767), Expect = 0.0
 Identities = 538/713 (75%), Positives = 609/713 (85%), Gaps = 4/713 (0%)

Query: 3   SRIPDFASVAYAADGFKAPPPPAGEPWMTPEGIPVKGFYGPEDREGCEGIDSFPGLPPYL 62
           S  PDF  +A+A     AP  P GE W TPEG+ V   +   D  G +    FPG+ P++
Sbjct: 2   STFPDFTKIAFAE--VPAPAAPKGEAWNTPEGVAVAPAFDASDVAGLDFTGGFPGVAPFV 59

Query: 63  RGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPR 122
           RGPYP MYVT PWT+RQYAGFSTAEDSNAFYRRNLAAGQ GLSVAFDLATHRGYDSDH R
Sbjct: 60  RGPYPTMYVTNPWTVRQYAGFSTAEDSNAFYRRNLAAGQMGLSVAFDLATHRGYDSDHER 119

Query: 123 VSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIVAAEEQGVPPEK 182
           V GDVGMAGVAIDSI DMRTLFSGIPLD+M+VSMTMNGAVLP +ALYIVAAEEQGV P+K
Sbjct: 120 VKGDVGMAGVAIDSILDMRTLFSGIPLDKMSVSMTMNGAVLPILALYIVAAEEQGVSPDK 179

Query: 183 LAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISISGYHMQEAGAT 242
           L+GTIQNDILKEFMVRNTYIYPP  SMRIISDIF +TS NMPKFNSISISGYHMQEAGAT
Sbjct: 180 LSGTIQNDILKEFMVRNTYIYPPAPSMRIISDIFAFTSANMPKFNSISISGYHMQEAGAT 239

Query: 243 QDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAKMRAARLIWAKL 302
            DLELAYTLADGVEY +AG+AAG++IDQFAPRLSFFWAIGMN+FME+AKMRAARL+WA+L
Sbjct: 240 ADLELAYTLADGVEYARAGVAAGMSIDQFAPRLSFFWAIGMNYFMEVAKMRAARLLWARL 299

Query: 303 VK-EFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGTQSLHTNALDE 361
           +K EF+PK D+SL LRTHSQTSGWSL AQDVFNNV RTC+EAMAA  G TQSLHTN+LDE
Sbjct: 300 MKREFDPKDDRSLSLRTHSQTSGWSLAAQDVFNNVARTCVEAMAAVNGQTQSLHTNSLDE 359

Query: 362 ALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARAWEHIREVEAL 421
           ALALPTDFSARI+RNTQLFLQ ESGTTR+ DPWGGSYYVERLT ++A +A  HI EVEAL
Sbjct: 360 ALALPTDFSARISRNTQLFLQMESGTTRVADPWGGSYYVERLTYELAQKALAHIEEVEAL 419

Query: 422 GGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDLLRVDNADVRA 481
           GGMAKAIE G+PKLRIEEAAAR QARIDSG+Q++VG+N+YKP+    I +L+VDN  VRA
Sbjct: 420 GGMAKAIEQGLPKLRIEEAAARTQARIDSGKQSVVGVNRYKPEVADDIPVLKVDNGAVRA 479

Query: 482 KQIDKLKRLRAERNQADVDAALAALTKAADGEGNLLELAVNAARAKATVGEISEALEKAW 541
           +Q++KL RL+AER+ A  +AAL AL   A G+GNLL LAV+AARAKATVGEIS ALEK +
Sbjct: 480 QQLEKLARLKAERDPAATEAALTALEDGARGDGNLLALAVDAARAKATVGEISYALEKVF 539

Query: 542 GRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAKMGQDGHDRGQK 601
           GRHRA+I+SI GVY +E G   P   + + +VEAFE+ DGRRPRIL+AKMGQDGHDRGQK
Sbjct: 540 GRHRAEIKSIQGVYMKEAGN-DPTAARAKAMVEAFEQADGRRPRILIAKMGQDGHDRGQK 598

Query: 602 VIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTLVPELKAALKQE 661
           VIA+AFADLGFDVDIGPLF TP EAARQAVENDVH+VG SSLAAGHLTL PELKA L ++
Sbjct: 599 VIATAFADLGFDVDIGPLFQTPAEAARQAVENDVHVVGASSLAAGHLTLAPELKAELAKQ 658

Query: 662 GRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNTRLGY 714
           GRDD+++VVGGVIPP D+ AL  AGA+AIFPPGTVIAEAA+ LL +LN +LGY
Sbjct: 659 GRDDILMVVGGVIPPQDFQALRDAGAAAIFPPGTVIAEAAIELLEQLNRQLGY 711


Lambda     K      H
   0.318    0.134    0.391 

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: 1363
Number of extensions: 43
Number of successful extensions: 3
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: 721
Length of database: 714
Length adjustment: 40
Effective length of query: 681
Effective length of database: 674
Effective search space:   458994
Effective search space used:   458994
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 (21.7 bits)
S2: 55 (25.8 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, 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

GapMind for catabolism of small carbon sources