Alignments for a candidate for pccA in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Mesorhizobium ciceri WSM1271

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate YP_004144009.1 Mesci_4850 carbamoyl-phosphate synthase L chain ATP-binding protein

Query= reanno::PS:Dsui_0516
         (663 letters)



>NCBI__GCF_000185905.1:YP_004144009.1
          Length = 660

 Score =  482 bits (1241), Expect = e-140
 Identities = 300/692 (43%), Positives = 401/692 (57%), Gaps = 74/692 (10%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MF KILIANRGEIACRVI+TARK+G++TVA+YS+AD  +L VEMADEAV IG +   ESY
Sbjct: 1   MFAKILIANRGEIACRVIRTARKLGVRTVAIYSDADAKSLHVEMADEAVHIGASPVGESY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           L  DKIIAA   TGA+A+HPGYGFLSEN +F  ++   G+ FIGP   SI  MG K  +K
Sbjct: 61  LRGDKIIAAALATGAQAIHPGYGFLSENPDFVDQVTAAGLIFIGPSAASIRAMGLKDAAK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
           +L  +A V  +PGY+            A++IGYPV+IKA AGGGGKG+R   +  E  E 
Sbjct: 121 RLMEKAGVPVVPGYHGEAQEIVLLASKAREIGYPVLIKARAGGGGKGMRRVEHPDEFSEA 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
            SS   EA+ +FGDDRV +EKYV +PRH+E+QV GD+ GN V+L ERDCS QRRHQKVIE
Sbjct: 181 LSSARREAKAAFGDDRVLVEKYVDKPRHVEVQVFGDNLGNVVHLYERDCSAQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGA----TKEFYFLEMNTRLQV 296
           E+P+P + P +RKAM E AV  A+A+NY  AGT+EF+V  +       F+F+EMNTRLQV
Sbjct: 241 ESPAPGMTPALRKAMTEAAVKAAKAINYSGAGTIEFIVDASQGLKADRFWFMEMNTRLQV 300

Query: 297 EHPVTELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRL 356
           EHPVTE++TG DLVE  +RVA GEKLP TQ+++ + G A E RI AED  +GFLP+TG L
Sbjct: 301 EHPVTEMVTGTDLVEWQLRVASGEKLPKTQSEIALVGHAFEARIYAEDAAKGFLPATGTL 360

Query: 357 --VKFQPPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFV 414
             +KF   A     +R++TGV  G  IS YYD MIAKL+VH   R+ A+  +  AL+   
Sbjct: 361 HHLKFPDAAPQGATIRIETGVRAGDAISPYYDPMIAKLVVHATDRQAALEALGAALSRTE 420

Query: 415 IRGISSNIPFQAALMQHARFQSGIFDTGFIAKEY--------------------PKGFDA 454
           I G + N  F AAL     F +G  DT  IA+                        G  A
Sbjct: 421 IAGSTVNTAFLAALAADPDFAAGDVDTSLIARHQTALTEVAPPTGETIAAAAVAASGAGA 480

Query: 455 SMVPHDDPALLIGVAAFVHRRYIDRAAQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPI 514
           S  P+D  + L G   + H   + R  ++         K G++ +V +   RH       
Sbjct: 481 SPSPNDPWSSLAG---YAHFHSVARRTRL---------KFGEDEIVAKVSVRH------- 521

Query: 515 EGGYLVTYNGEKYELLSDWRQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADM--- 571
           +G + VT + + Y+                N  +F       R T +L  W     +   
Sbjct: 522 DGRFQVTLD-KPYD--------------DTNSHDF-------RSTPRLARWPGHITLFEG 559

Query: 572 -MVMSARAAELLALMPEKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKM 630
            +  +    + LA   E AA   S  L +PMPGL++ V V  G  V  G+ L ++EAMKM
Sbjct: 560 AVGYTFTVPDPLARADEAAAG--SGSLRAPMPGLVKLVRVGKGDAVIKGQPLLILEAMKM 617

Query: 631 ENILKAEQDCKVKKISVTAGSSLSVDEIIIEF 662
           E+ + A  D  + +I+ T G  ++   +++ F
Sbjct: 618 EHTIAAPHDGVIAEIA-TEGVQVTDGTVLVRF 648


Lambda     K      H
   0.319    0.135    0.391 

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: 1087
Number of extensions: 46
Number of successful extensions: 5
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: 663
Length of database: 660
Length adjustment: 38
Effective length of query: 625
Effective length of database: 622
Effective search space:   388750
Effective search space used:   388750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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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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
the source code
instructions for running GapMind on your computer

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