Aligments for a candidate for pccA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22345 HSERO_RS22345 urea
           carboxylase
          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.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources