GapMind for catabolism of small carbon sources

 

Alignments 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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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