Alignments for a candidate for liuB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Caulobacter crescentus NA1000

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CCNA_02261 CCNA_02261 propionyl-CoA carboxylase biotin-containing subunit

Query= reanno::Smeli:SM_b21124
         (662 letters)



>FitnessBrowser__Caulo:CCNA_02261
          Length = 669

 Score =  479 bits (1233), Expect = e-139
 Identities = 293/677 (43%), Positives = 395/677 (58%), Gaps = 34/677 (5%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MFSK+LIANRGEIA R+I+T RRLGI+TV VYSDAD  +L V +ADE + IG +PA +SY
Sbjct: 1   MFSKILIANRGEIAVRVIKTCRRLGIKTVVVYSDADAGSLAVEMADETVHIGASPANQSY 60

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           L +  I+ A +  GAQA+HPG+GFLSENA FA+  A+ G++F+GP P AI AMG K  +K
Sbjct: 61  LVADKIIAACKQTGAQAVHPGFGFLSENAGFAQRCADEGIVFIGPNPGAISAMGDKIESK 120

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
              + +GV  VPG+ GE  D +     + EIGYPV+IKA AGGGGKG+R    ++D    
Sbjct: 121 KFAQAAGVSCVPGHIGEIADTAEAVKISEEIGYPVMIKASAGGGGKGIRVAWTRKDVEEG 180

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
             A R EA+++FGD  + +E+++  PRHIE+QV GD+HGN+VHLFER+CS+QRR+QKVIE
Sbjct: 181 FPAVRAEAKASFGDDRIFIEKFIESPRHIEIQVLGDKHGNVVHLFERECSIQRRNQKVIE 240

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300
           EAP+P +    R AMG  AV  A+A+ Y  AGTVEF+A          F+F+EMNTRLQV
Sbjct: 241 EAPSPLLDEATRNAMGAQAVALAKAVNYDSAGTVEFVAGQDKS-----FFFLEMNTRLQV 295

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EHPVTE ITG+DLVE  +R A GE +   Q+D+S+NGWA E+R+YAEDP R FLP+ GRL
Sbjct: 296 EHPVTELITGLDLVEQMIRSAYGEKMAFGQSDLSINGWAIESRIYAEDPYRKFLPSIGRL 355

Query: 361 TELSFP-EGTS---------RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDA 410
                P EG           R D+GVR+GD I+ +YDP+I+KL      R AA+  +  A
Sbjct: 356 VRYDPPAEGDKDGPNGGYVVRNDAGVREGDEISMFYDPMISKLCTWAPTRLAAIDGMGRA 415

Query: 411 LKECRIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIE---RLTAPVAPGDEAL---- 463
           L++  I G   N  FL  + +E  FRSG   T  I  E       T P A   + L    
Sbjct: 416 LEDFHIEGLGQNIPFLAAVMDEERFRSGKLATSYIKDEFPDGFNGTTPTAVQLDILTAVG 475

Query: 464 -ALAAIFSTGALDPNRSTDPWSSLGSWQI-WGDAHRMVVIEHADVRATVTLASRGRDQFA 521
            A+  +++T A     S     +   W +  G+    V +   D    V L   GR  F 
Sbjct: 476 AAMQRVYATRARS-YESGLIGEARDEWVVAIGETRLRVKVGGEDGAVAVELLDEGRTLFL 534

Query: 522 V----RAGASTLPVLVLDRFEGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDG 577
                R G       VL+      +   A +   IR  R  +   L    R+   H  D 
Sbjct: 535 TDIDWRPGKPVFKA-VLNGLAFTVQAAPAAEGFTIR-HRAAKTRVLVLTPRSAELH--DK 590

Query: 578 LTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIA 637
           L   Q+++     +++PMPGLV  + V  G  V +G+ + V+EAMKM+  + A R+G + 
Sbjct: 591 LPEKQAAD-TSKLVLSPMPGLVVSMDVTTGQQVREGEVVCVLEAMKMQNIIRAERDGVVK 649

Query: 638 NVHVAEGAQVSEGTVLV 654
            V+   G  V+   VLV
Sbjct: 650 AVNAKGGDPVAADEVLV 666


Lambda     K      H
   0.319    0.135    0.394 

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: 1159
Number of extensions: 48
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 662
Length of database: 669
Length adjustment: 38
Effective length of query: 624
Effective length of database: 631
Effective search space:   393744
Effective search space used:   393744
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 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:

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
the source code
instructions for running GapMind on your computer

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