Aligments for a candidate for liuD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for liuD in Acidovorax sp. GW101-3H11

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ac3H11_1923 Geranyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.5)

Query= BRENDA::Q9I297
         (535 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1923
          Length = 537

 Score =  442 bits (1137), Expect = e-128
 Identities = 254/548 (46%), Positives = 336/548 (61%), Gaps = 27/548 (4%)

Query: 2   AILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARH----SARGKLLVR 57
           A+  ++ NP SAE     A +  +++ALR L     E   +AA AR       RG+LL R
Sbjct: 3   AVFTSRFNPGSAEATQRRAALQARLDALRAL-----EERAAAASARSLPQFEKRGQLLPR 57

Query: 58  ERINRLLDPGSPFLELSALAAH--EVYGEE--VAAAGIVAGIGRVEGVECMIVGNDATVK 113
           +R+  LLD G+P+L L  LA +  +V   E  V   G+VAGIG V GV CM+V +D+ ++
Sbjct: 58  QRVALLLDAGAPWLPLCTLAGYLQDVKDPEKSVPGGGMVAGIGFVSGVRCMVVASDSGIE 117

Query: 114 GGTYYPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPR-QDEVFPDREHFGRIFFNQAN 172
            G   P+ ++K LR Q IAL+NRLP I+LV+S GANL R + E F    H G +F N A 
Sbjct: 118 AGAIQPMGLEKILRVQEIALQNRLPFIHLVESAGANLMRYRVEGFV---HGGTLFRNLAR 174

Query: 173 MSARGIPQIAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEEL 232
           +SA GIP I V  GS TAGGAY+P +SD  +MV+ ++  FLAGPPL+KAATGE+ + EEL
Sbjct: 175 LSAAGIPVITVQHGSGTAGGAYMPGLSDVVIMVQGRSRAFLAGPPLLKAATGEIATEEEL 234

Query: 233 GGADVHCKVSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQCRAPRAP--LYPAEELY 290
           GGA++H  VSG+ ++ A+DD  A+ +AR  VA L W        R P AP  L PA++L 
Sbjct: 235 GGAEMHTAVSGLGEYLAQDDREAIGLARDVVAQLGWNMP-----RRPSAPVPLLPADDLL 289

Query: 291 GVIPADSKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFA 350
            ++ AD +QP D+REV+ARLVDGSE  EFKA +G   VC   H+ G+ +  ++NNG +  
Sbjct: 290 SLMSADLRQPVDMREVMARLVDGSELLEFKARYGMATVCAQGHIGGHAVGFISNNGPIDV 349

Query: 351 EAAQKGAHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFT 410
             A K  HFI+  CQ G P+++LQN TG+MVG+  E GG+ KHG+K++ AV  A VP+ T
Sbjct: 350 AGANKATHFIQWMCQLGHPIIYLQNTTGYMVGKDSEQGGMIKHGSKMIQAVTNATVPQIT 409

Query: 411 VLIGGSFGAGNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLG 470
           +  G SFGAGNYGMCGR Y PRFL+ WP A+  VMGGEQAA  +  V      R G    
Sbjct: 410 IQCGASFGAGNYGMCGRGYAPRFLFSWPGAKTAVMGGEQAARTMQIVTEAALARKGITPD 469

Query: 471 VEEEAKIKAPILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNA---PIEP 527
             E       I+  +E Q   +Y+S  L DDGVIDP  TR VLA  L     A    + P
Sbjct: 470 PAESQAQFDKIVAMFEAQADVFYTSGLLLDDGVIDPRDTRAVLAFCLDTCAEAQARTLRP 529

Query: 528 TAFGVFRM 535
            +FGV RM
Sbjct: 530 LSFGVARM 537


Lambda     K      H
   0.321    0.137    0.409 

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: 705
Number of extensions: 32
Number of successful extensions: 6
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: 535
Length of database: 537
Length adjustment: 35
Effective length of query: 500
Effective length of database: 502
Effective search space:   251000
Effective search space used:   251000
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 (21.9 bits)
S2: 52 (24.6 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