Alignments for a candidate for prpE in Cereibacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Cereibacter sphaeroides ATCC 17029

Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011840264.1 RSPH17029_RS01250 propionyl-CoA synthetase

Query= metacyc::MONOMER-21334
         (629 letters)



>NCBI__GCF_000015985.1:WP_011840264.1
          Length = 630

 Score = 1038 bits (2684), Expect = 0.0
 Identities = 495/629 (78%), Positives = 550/629 (87%)

Query: 1   MAYQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDR 60
           MAY  +Y+    DP  FWM+AA+ IDWV  PS+AL D   P YEWF D +VN CWNAVDR
Sbjct: 1   MAYASLYKWSLEDPNGFWMKAAEQIDWVSPPSKALFDEKEPFYEWFADGQVNACWNAVDR 60

Query: 61  HVEAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIP 120
           HVEAGRG+Q AI+++SPITH+ + I+Y EL+ RVA LAGALRAKGVEKGDRVIIYMPMIP
Sbjct: 61  HVEAGRGKQIAIVHESPITHSSKGITYAELQARVASLAGALRAKGVEKGDRVIIYMPMIP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLD 180
           EALEAMLACARLGA+HSVVFGGFAA+ELAVRIDD  PKAIIAASCGLEP RVVHYKPLLD
Sbjct: 121 EALEAMLACARLGAIHSVVFGGFAAHELAVRIDDCTPKAIIAASCGLEPSRVVHYKPLLD 180

Query: 181 GAIDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
            AI+ A HKP+FCVIFQREQEVA L EGRD  WH FQYGVEPAECVPVEGNHPAYILYTS
Sbjct: 181 QAIEEATHKPDFCVIFQREQEVAKLIEGRDVAWHTFQYGVEPAECVPVEGNHPAYILYTS 240

Query: 241 GTTGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTG PKGV+R T GHLVALNWTMK IY++D GDVFWAASDVGWVVGHSYICYGPLI G 
Sbjct: 241 GTTGQPKGVVRATGGHLVALNWTMKAIYDIDAGDVFWAASDVGWVVGHSYICYGPLIAGA 300

Query: 301 TTIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKA 360
           TTIV+EGKPVGTPDAG FWRV+  HKVK+FFTAPTA+RA+KREDP+G ++  Y+L +LKA
Sbjct: 301 TTIVYEGKPVGTPDAGAFWRVMQNHKVKTFFTAPTALRAIKREDPQGALIQDYNLRNLKA 360

Query: 361 LYLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPG 420
           L+LAGERADPDTI+WAQK + VPVIDHWWQTE+GW +A NPLGIE LP K+GSP+  MPG
Sbjct: 361 LFLAGERADPDTIVWAQKNVGVPVIDHWWQTESGWAMAANPLGIEALPVKIGSPSLPMPG 420

Query: 421 YDVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAG 480
           YDV++LDEGGHQ++ G+LGAIA+KLPLPPGTLP LWNA+ RF KSYL HFPGYYETGDAG
Sbjct: 421 YDVRVLDEGGHQLEAGQLGAIAIKLPLPPGTLPTLWNAQDRFVKSYLTHFPGYYETGDAG 480

Query: 481 MIDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGF 540
            IDEDGY+YIMARTDDVINVAGHRLSTG MEEVLA HEDVAECAVIGV+D LKGQ PLGF
Sbjct: 481 YIDEDGYIYIMARTDDVINVAGHRLSTGAMEEVLASHEDVAECAVIGVTDALKGQSPLGF 540

Query: 541 LCLNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADG 600
           LCLN G NR   DVVKE VKLVR+KIGPVA FK A VVDRLPKTRSGKILRGTMV IADG
Sbjct: 541 LCLNKGSNRAAEDVVKECVKLVREKIGPVADFKRACVVDRLPKTRSGKILRGTMVKIADG 600

Query: 601 KEYKMPATIDDPAILDEIKVALQSLGYAK 629
           +E+KMPATIDDPAILDEI+VAL+++GY +
Sbjct: 601 QEFKMPATIDDPAILDEIRVALEAVGYPR 629


Lambda     K      H
   0.319    0.137    0.428 

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: 1549
Number of extensions: 44
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 629
Length of database: 630
Length adjustment: 38
Effective length of query: 591
Effective length of database: 592
Effective search space:   349872
Effective search space used:   349872
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 Apr 16 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis