Alignments for a candidate for pccA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Rhodomicrobium vannielii ATCC 17100

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_013420985.1 RVAN_RS17280 carbamoyl-phosphate synthase subunit L

Query= reanno::Dino:3607308
         (681 letters)



>NCBI__GCF_000166055.1:WP_013420985.1
          Length = 663

 Score =  472 bits (1215), Expect = e-137
 Identities = 277/702 (39%), Positives = 388/702 (55%), Gaps = 75/702 (10%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYI 61
           F+K+LIANRGEIACR+++TAR MG +TVA++SDAD +A+H R ADEAV IGPSP  +SY+
Sbjct: 6   FRKLLIANRGEIACRIVRTARAMGYRTVAVFSDADADAMHTRAADEAVRIGPSPPRESYL 65

Query: 62  VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121
            I +++DA ++TGA+A+HPGYGFL+EN  FAEA E  G+ F+GPPA  I AMGDK  +K 
Sbjct: 66  DIARILDAAKKTGADAIHPGYGFLAENADFAEACEAAGLVFVGPPARVIRAMGDKAAAKA 125

Query: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGF 181
           IA+ A +  VPGY G           +  IG+P+++KA AGGGG+G+R     AE  +  
Sbjct: 126 IAEAAGLPCVPGYRGEDQADARLTAEAAAIGFPLLVKAVAGGGGRGIRAVHAAAELPDAL 185

Query: 182 QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEE 241
            +++ EA  +FGDDR+ +E+ + +PRH+E+Q+  D HGN ++L ER+CS QRR QK++EE
Sbjct: 186 AAAQREAKAAFGDDRLMLERLIERPRHLEVQIFGDDHGNVVHLFERDCSTQRRRQKIIEE 245

Query: 242 APSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVTE 301
           APSP L  A R+ +   + ALAQA GY +AGTVEFI D D  FYFLEMNTRLQVEHPVTE
Sbjct: 246 APSPVLTPAHRERLTGYAVALAQAAGYRNAGTVEFIADADLTFYFLEMNTRLQVEHPVTE 305

Query: 302 LITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPP 361
           ++ GVDLV+  +RVAAGE LP+ QD++ + G AIE RL AEDPY  F P  G +  +   
Sbjct: 306 MVVGVDLVDWQLRVAAGEPLPLRQDEIAMRGHAIEARLCAEDPYDGFRPQAGTVIHF--- 362

Query: 362 VEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIE 421
                            AP     +R DTGV  G E+S +YD M+AK    G DR  A  
Sbjct: 363 -----------------APQERGGIRFDTGVETGSEVSPWYDSMVAKAIAGGRDRLEATR 405

Query: 422 AMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTR 481
            + +AL+   + G+  N  F+ A++    F + E+ T  + +                  
Sbjct: 406 RLASALEDAPLLGLATNREFLVALLRGEAFDRAEIATTTLDDW----------------- 448

Query: 482 LAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTA---------------QDARFDV 526
             A  AA    +   R R S T          DW + A                 + FD 
Sbjct: 449 --AQTAAHDAASPFARPRPSPT----------DWALAAALSAERGGGAGEWFWSGSAFDF 496

Query: 527 TIDADPGGSTVRFADGTAHRV--TSRWTPGDSLATVEIDGAP--MVLKVDKITSGFRMRF 582
           ++D   GG T R    T  R    +    G+ +    I+ AP  +V + D +       +
Sbjct: 497 SLDLTCGGETKRLTY-TRRRSGPLAVAVDGERIEIALIENAPPRIVFEADGVRRRAAAAW 555

Query: 583 RGADVKVHVRTPRQAELNDLMPEKLPPDTSK---MLLCPMPGLVVKIDVEVGDEVQEGQA 639
           +GA + + V     A      P+    D +     +  P+ GL+VK+  E G  V  G  
Sbjct: 556 QGATLHLAVD---DAAFAFAEPDHAHADDAADGARIAAPVAGLLVKVLAEPGQAVAAGDT 612

Query: 640 LCTVEAMKMENILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681
           L  +EAMKME  + A  +  +  ++A AG  +A   ++ E E
Sbjct: 613 LAIIEAMKMETRVTALASGRIAAVHATAGAQVASGALLFEIE 654


Lambda     K      H
   0.318    0.134    0.392 

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: 1149
Number of extensions: 46
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 681
Length of database: 663
Length adjustment: 39
Effective length of query: 642
Effective length of database: 624
Effective search space:   400608
Effective search space used:   400608
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:

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