GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Herbaspirillum aquaticum IEH 4430

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_088756563.1 CEJ45_RS18815 urea carboxylase

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_002213425.1:WP_088756563.1
          Length = 1207

 Score =  390 bits (1001), Expect = e-112
 Identities = 216/461 (46%), Positives = 290/461 (62%), Gaps = 22/461 (4%)

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

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

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
            +A+E  V  + G   L+E+  +A+  + ++GYPVM+K++AGGGG GMR+  +D E  + 
Sbjct: 121 ALAREQGVPMLEG-TDLLENIGDALAAAARVGYPVMLKSTAGGGGIGMRVCRSDAELGDA 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 E    A+   A+ LAKAV Y SAGTVEF+ D     FYFLE+NTRLQVEH V
Sbjct: 240 ETPAPNLPEGMADALCAAAIKLAKAVNYRSAGTVEFVYDSLAGQFYFLEVNTRLQVEHGV 299

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

Query: 358 YRPPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRA 417
              PA                  +   A+R DT V  G EI  Y+DPMIAKL +W PTR 
Sbjct: 360 VDFPA------------------ADGQALRIDTWVEAGCEIPPYFDPMIAKLISWQPTRE 401

Query: 418 AAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTT 458
           AA  A+  AL    + G+  N  +L  ++D   F  G   T
Sbjct: 402 AARVALNSALRETALYGVETNQHYLRQILDDVPFARGQPWT 442



 Score = 42.4 bits (98), Expect = 1e-07
 Identities = 20/64 (31%), Positives = 36/64 (56%)

Query: 618  PMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVVAKINASAGNSLAVDDVI 677
            P+ G + +V V  GQ V +G+ L  +E+MKME  + A + G+VA++    G+ +     +
Sbjct: 1137 PIAGNLWQVKVSPGQRVAQGELLMILESMKMEINITAPEAGIVAEVRVQPGSPVRAGQCV 1196

Query: 678  MEFE 681
            +  E
Sbjct: 1197 LVME 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: 1846
Number of extensions: 87
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
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 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