GapMind for catabolism of small carbon sources

 

Alignments 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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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