Alignments for a candidate for liuB in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Ruegeria conchae TW15

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_010441939.1 G7G_RS0113355 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000192475.1:WP_010441939.1
          Length = 681

 Score =  480 bits (1236), Expect = e-140
 Identities = 290/702 (41%), Positives = 398/702 (56%), Gaps = 72/702 (10%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MF+K+LIANRGEIACR+I+TAR++GI TVA+YSDAD +ALHV++ADEA+ IG  PA +SY
Sbjct: 1   MFNKILIANRGEIACRVIKTARKMGIGTVAIYSDADRNALHVSMADEAVHIGPPPANQSY 60

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           +    ++ A R  GAQA+HPGYGFLSEN+ FAEA+   G+ FVGPP  AI +MG K  +K
Sbjct: 61  IVIDKVMDAIRQSGAQAVHPGYGFLSENSKFAEALDAEGVAFVGPPVGAIESMGDKITSK 120

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
            + + +GV  VPGY G  +DA      + +IGYPV+IKA AGGGGKGMR     E+    
Sbjct: 121 KIAQEAGVSTVPGYMGLIEDADEAVKISNDIGYPVMIKASAGGGGKGMRIAWNDEEAREG 180

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
            ++++ EA ++FGD  + +E+++T+PRHIE+QV  D HGN ++L ER+CS+QRR+QKV+E
Sbjct: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300
           EAP+P +  E R+AMG+ AV  A+A+ Y  AGTVEFI D        +FYF+EMNTRLQV
Sbjct: 241 EAPSPFLDPETRKAMGEQAVALAKAVDYASAGTVEFIVDGEK-----NFYFLEMNTRLQV 295

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EHPVTE ITG+DLVE  +RVA+GE L   Q ++++ GWA E RLYAEDP RGFLP+ GRL
Sbjct: 296 EHPVTELITGVDLVEQMIRVAAGEKLTITQDNVTLTGWAIENRLYAEDPYRGFLPSIGRL 355

Query: 361 TEL-------------------SFPEGTSRV--DSGVRQGDTITPYYDPLIAKLIVHGQN 399
           T                       P+G S V  D+GV +G  I+ YYDP+IAKL      
Sbjct: 356 TRYRPPQEIAAGPLLVNDKWQGDAPKGDSAVRNDTGVYEGGEISMYYDPMIAKLCTWAPT 415

Query: 400 RSAALGRLQDALKECRIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDRE----------- 448
           R  A+  ++ AL    + G   N  FL  + +   F SG   T  I  E           
Sbjct: 416 REQAIEAMRVALDSFEVEGIGHNLPFLSAVMDHPKFVSGDMTTAFIAEEYPDGFEGVELP 475

Query: 449 ---IERLTAPVAPGDEALALAAIFSTGALDPNR---STDPWSSLGSWQIWGDAHRMVVIE 502
              + R+ A  A       +     +G +D +     TD   SL   +        V IE
Sbjct: 476 EADLRRVAASCAAMHRVAEIRRTRVSGRMDNHERKVGTDWVVSLQGQEF------EVAIE 529

Query: 503 HADVRATVTLASRGR----------DQFAVRAGASTLPVLVLDRFEGGARLEVAGQKRLI 552
                +TV+ A   +          DQ AV     +  VL + +  GG R+   G    +
Sbjct: 530 ADQDGSTVSFADGTKHRVASDWTPGDQLAVLDVDGSPLVLKVGKVSGGFRVRNRGADLKV 589

Query: 553 RFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTK 612
                R+A         L   +P+ L    S       L+ PMPGL+  + V  G  V +
Sbjct: 590 HVRTPRQA--------ELARMMPEKLPPDTSKM-----LLCPMPGLIVKIDVEVGQEVQE 636

Query: 613 GQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLV 654
           GQAL  +EAMKME  L A ++G ++ ++   G  ++   V++
Sbjct: 637 GQALCTVEAMKMENILRAEKKGVVSKINAGPGDSLAVDDVII 678


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: 1122
Number of extensions: 64
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 662
Length of database: 681
Length adjustment: 39
Effective length of query: 623
Effective length of database: 642
Effective search space:   399966
Effective search space used:   399966
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 24 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