GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudovibrio axinellae Ad2

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_068006658.1 PsAD2_RS13240 biotin/lipoyl-binding protein

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_001623255.1:WP_068006658.1
          Length = 629

 Score =  449 bits (1156), Expect = e-130
 Identities = 277/684 (40%), Positives = 382/684 (55%), Gaps = 62/684 (9%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF+ +L+ANRGEIA RV +TAR+ G  ++A+YS+AD  A HV  AD A  IG     +SY
Sbjct: 1   MFDSVLVANRGEIARRVFRTARQKGYRSIAVYSEADATAPHVGDADVAACIGGATPAESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           + I+ V+ A R TGAQAVHPGYGFL+EN+ FA+A +A G++FVGPP  AIE MG K  SK
Sbjct: 61  LNIEAVLEAARKTGAQAVHPGYGFLAENADFAKACDAAGLVFVGPPAQAIELMGSKRLSK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
               EA V  VPGY G  +  +     + +IG P+MIKASAGGGG+G+R+  N +   + 
Sbjct: 121 LRMIEAGVPCVPGYSGADQSTEVLAAEAARIGVPLMIKASAGGGGRGLRLVENLEGLEDK 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
             ++ +EA  +FG+  + +EK V  PRH+EIQ+  D+HGN ++LGER+CS+QRR+QKV+E
Sbjct: 181 LAAAASEAVGAFGNGELILEKAVINPRHVEIQIFADNHGNVVHLGERDCSVQRRHQKVIE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAP P +    R AMG+ AV  A+A+GY  AGTVEF++    +FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPGPSVTPEIRDAMGQAAVEAARAIGYRGAGTVEFLLAADGSFYFMEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           E ITG DLV   + VAAG+PL + Q D+  +G A+E RLYAED   GFLP  G++  +  
Sbjct: 301 EEITGQDLVAWQLDVAAGKPLPLAQEDISFSGHAMELRLYAEDADAGFLPQTGQVVAWNG 360

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           P                     E A+R D+ + +G  IS YYDPMIAKL      R  A 
Sbjct: 361 P---------------------ELALRVDSAIEQGSVISSYYDPMIAKLIAHGADREEAR 399

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
             +   LD   ++G+ HN  FL +V+    F +G+ TTAF             L + +L 
Sbjct: 400 RKLLRGLDQLVLQGLVHNGSFLKSVLLDDVFAAGEATTAF-------------LNDRELG 446

Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVSFD 540
            VAA +     V E+ R         ++ +  T W         PV I  D +  T   D
Sbjct: 447 SVAADS-----VRELMRDLAVHLFARNKGQ--TRWTT---ATPLPVKIKLDGESVTPRED 496

Query: 541 DGSSMRVTSDWTPGDQLANLM--VDGAPLVLKVGK-ISGGFRIRTRGADLKVHVRTPRQA 597
               +++       D L  L+  VDG      V K   GGF I   G       +T    
Sbjct: 497 ----LQILEQ----DDLGKLVFYVDGVRRSAFVSKGPEGGFWISLDG-------QTQFFE 541

Query: 598 ELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKK 657
           E +    +     TS  ++ PMPG +V +  E G +V +G  L  +EAMKM++ L A + 
Sbjct: 542 EQSLSTRKTDNSATSSSVIAPMPGAVVALKTEQGAQVSKGDVLLVLEAMKMQHELTAPRD 601

Query: 658 GVVAKINASAGNSLAVDDVIMEFE 681
           G+VA++    G  +   DV++  E
Sbjct: 602 GIVAELGTQEGAQVNSRDVLVRLE 625


Lambda     K      H
   0.317    0.134    0.387 

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: 950
Number of extensions: 37
Number of successful extensions: 3
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: 681
Length of database: 629
Length adjustment: 38
Effective length of query: 643
Effective length of database: 591
Effective search space:   380013
Effective search space used:   380013
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: 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:

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