GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Amycolatopsis halophila YIM 93223

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_034277971.1 AMYHA_RS19150 acyl-CoA carboxylase subunit beta

Query= SwissProt::I3R7F1
         (516 letters)



>NCBI__GCF_000504245.1:WP_034277971.1
          Length = 512

 Score =  586 bits (1510), Expect = e-172
 Identities = 289/506 (57%), Positives = 368/506 (72%), Gaps = 1/506 (0%)

Query: 11  REKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEETK 70
           R +  + +  G    +  QHD GK TARER++  LD  +F E D +R H++    ++   
Sbjct: 8   RARLRDEITAGAPAAVRRQHDLGKRTARERLELLLDPDSFIEIDMYRRHQSSSATLKSRP 67

Query: 71  LPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLNDS 130
              DGV+ G G VDGR VFV+A DFT+FGGSLG+  A KI KVMD A+  GAP+I LNDS
Sbjct: 68  YT-DGVVAGSGTVDGRRVFVYAQDFTIFGGSLGQAQAAKIHKVMDHALATGAPLIALNDS 126

Query: 131 AGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRDTS 190
            GARIQEGV SL G+G IFRR+ EASGV+PQ+S IMGPCAGGA YSPAL DFTFMVR T+
Sbjct: 127 GGARIQEGVLSLHGYGGIFRRHVEASGVIPQLSVIMGPCAGGAAYSPALADFTFMVRGTA 186

Query: 191 HMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLPQN 250
            M++TGPDV+  V+GE V+ DELGGA  H S SGVA    D EE  LDD+R+LLS LP N
Sbjct: 187 QMYLTGPDVVAAVSGERVSHDELGGADVHGSRSGVATLVYDDEESCLDDVRYLLSLLPAN 246

Query: 251 NVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKNIV 310
           N++ PPR    D  +     L +IVP +P +PYD+ DV+  ++D+G FF + ED+A+N++
Sbjct: 247 NLDVPPRAPAPDAEQDERPALADIVPVEPNQPYDMRDVVAEIVDDGEFFELHEDWAQNVI 306

Query: 311 VGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLPGT 370
            G GR+ G  VGIV NQP+V AG LD  AS+K ARF+RFCD+FNIP+++ VDVPGFLPGT
Sbjct: 307 CGLGRIGGDVVGIVGNQPQVLAGVLDRVASQKAARFVRFCDAFNIPLVTLVDVPGFLPGT 366

Query: 371 DQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAEIA 430
           +QE+ G+IRHGA+LLYAY EA+VP + VI RKAYGGAY VM S+ +G D++ AWPT EIA
Sbjct: 367 EQEYAGVIRHGAQLLYAYCEASVPRIQVILRKAYGGAYIVMDSRSIGTDLSLAWPTNEIA 426

Query: 431 VMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDTRN 490
           VMG +GAVNIL+R +L AADD   RR EL+ EY +EF +P+ AA+RG VDDVI+P  TR 
Sbjct: 427 VMGAEGAVNILHRKDLAAADDAAERRAELVAEYTDEFMHPHYAAERGLVDDVIDPAQTRA 486

Query: 491 RLIADLRMLKSKRKSQPDKKHGNIPL 516
            +   L ML++KR+  P++KHGNIPL
Sbjct: 487 MVARGLAMLRTKRRRMPERKHGNIPL 512


Lambda     K      H
   0.318    0.138    0.407 

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: 801
Number of extensions: 38
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: 516
Length of database: 512
Length adjustment: 35
Effective length of query: 481
Effective length of database: 477
Effective search space:   229437
Effective search space used:   229437
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: 52 (24.6 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:

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