GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Herbaspirillum seropedicae SmR1

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate HSERO_RS22345 HSERO_RS22345 urea carboxylase

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__HerbieS:HSERO_RS22345
          Length = 1207

 Score =  391 bits (1005), Expect = e-113
 Identities = 242/592 (40%), Positives = 333/592 (56%), Gaps = 47/592 (7%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF+ +LIANRG IACR+++T R + ++ V +YS+AD  +LHV  AD A+ +G  PA Q+Y
Sbjct: 1   MFDHLLIANRGAIACRILRTLRTLDVTGVCVYSEADLGSLHVLQADRAISLGEGPAAQTY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           + +DK++AA R +GAQA+HPGYGFLSEN+ FAEA EA G+ FVGP    +   G K T++
Sbjct: 61  LAVDKILAAARDSGAQAIHPGYGFLSENAAFAEACEAAGIAFVGPTPAQLRIFGLKHTAR 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
            +A+E  V  + G   L+E  D+A+  ++++GYPVM+K++AGGGG GMR+  +D E  + 
Sbjct: 121 ALAREQGVPMLEG-TDLLESIDDALAAASRVGYPVMLKSTAGGGGIGMRVCRSDAELADA 179

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           F S +    N+F D  +FIEK++ + RH+E+QV  D  G  I LG R+CS+QRRNQKV+E
Sbjct: 180 FDSVRRLGQNNFSDAGVFIEKYIERARHLEVQVFGDGRGEVIALGVRDCSVQRRNQKVLE 239

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDG-QKNFYFLEMNTRLQVEHPV 299
           E P+P L +    A+   A+ LAKAV Y SAGTVEF+ D     FYFLE+NTRLQVEH V
Sbjct: 240 ETPAPNLPDGMAEALCAAAIKLAKAVNYRSAGTVEFVYDSLAGQFYFLEVNTRLQVEHGV 299

Query: 300 TELITGVDLVEQMIRVAAGE--PLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTR 357
           TE + GVDLV  MI +AAG+  PL+     ++  G AI+ RLYAEDP R F P  G LT 
Sbjct: 300 TEQVWGVDLVRWMIELAAGDLPPLAQLAAGLQPRGHAIQARLYAEDPGRQFQPCPGLLTA 359

Query: 358 YRPPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRA 417
              P                  P    A+R DT V  G EI+ Y+DPMIAKL +W PTR 
Sbjct: 360 VDFP------------------PVDGQALRIDTWVEAGCEIAPYFDPMIAKLISWQPTRE 401

Query: 418 AAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAE-EYPEGFEGVNLPE 476
           AA  A+  AL +  + G+  N  +L  ++    F SG   T  + +  Y      V  P 
Sbjct: 402 AARLALDAALRATLLYGVETNQHYLRQILADVPFASGQPWTRCLEQLVYRADTVEVLAPG 461

Query: 477 TDLR------RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAA 530
           T         R+   A  +           SG MD    R+G      L  A+    +  
Sbjct: 462 TQTTVQDHPGRIGYWAVGV---------PPSGPMDERALRLGNR---LLGNAEEAAGLEV 509

Query: 531 DHDGSTVSFDDGSSMRVTSDWTP------GDQLANLMVDGAPLVLKVGKISG 576
              G  + F+  + + VT    P         +A ++   A   LK+G ISG
Sbjct: 510 TMSGPILRFNTAAMVVVTGAVIPVLLDGVAQPMATVLHIAAGSTLKLGAISG 561



 Score = 43.1 bits (100), Expect = 8e-08
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 598  ELARLMPEKLPPDTSKMLL-CPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEK 656
            E + +  E  P    +M +  P+ G + +V V  GQ V +G+ L  +E+MKME  + A  
Sbjct: 1116 ESSAIAQEAAPLQDGQMAVDAPIAGNLWQVKVSPGQRVAQGELLMILESMKMEIHIAAPA 1175

Query: 657  KGVVAKINASAGNSLAVDDVIMEFE 681
             GVVA++    G+ +     ++  E
Sbjct: 1176 AGVVAEVRVQPGSPVRAGQCVLVME 1200


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: 1863
Number of extensions: 91
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: 2
Length of query: 681
Length of database: 1207
Length adjustment: 43
Effective length of query: 638
Effective length of database: 1164
Effective search space:   742632
Effective search space used:   742632
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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