Alignments for a candidate for prpE in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Magnetospirillum magneticum AMB-1

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011384701.1 AMB_RS11645 propionyl-CoA synthetase

Query= reanno::Phaeo:GFF1175
         (629 letters)



>NCBI__GCF_000009985.1:WP_011384701.1
          Length = 638

 Score =  864 bits (2232), Expect = 0.0
 Identities = 409/628 (65%), Positives = 495/628 (78%)

Query: 2   SYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRH 61
           +Y + YE    +PE FW EAA+ I W     K L D     Y WF  A  NTCYNAVDRH
Sbjct: 4   AYQQAYEKSLKDPEGFWGEAAKEIHWYKTWDKVLDDSKKPFYRWFVGAETNTCYNAVDRH 63

Query: 62  VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121
           VEQGRG QTAIIYDSP+T TKR+ISY EL+++V+ LAGA+ A GV KGDRV++YMPM+PE
Sbjct: 64  VEQGRGAQTAIIYDSPVTSTKRKISYDELKDQVSRLAGAMAALGVAKGDRVLLYMPMVPE 123

Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181
           A+  MLA ARLGA+HSVVFGGFA  ELA RI+DA PK I++ASCG+E  R + YKP+LD 
Sbjct: 124 AVVGMLAVARLGAIHSVVFGGFAPAELATRINDAKPKVILSASCGIEGSRVIAYKPMLDE 183

Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241
           AI L+ HKP   ++ QR Q VA + +  D++W       +PA+CVPV    P YILYTSG
Sbjct: 184 AIALSEHKPGHTIMLQRPQSVAVMDKAGDLDWTEVCAKAKPADCVPVLATDPLYILYTSG 243

Query: 242 TTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301
           TTGQPKGV+R   G +VAL W+MK +Y++ PG+VFWAASDVGWVVGHSYICY PL++G+T
Sbjct: 244 TTGQPKGVVRDNGGHMVALMWSMKYVYDIKPGEVFWAASDVGWVVGHSYICYAPLLNGST 303

Query: 302 TIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQV 361
           T+V+EGKP+GTPDAG FWR+ISE+K+ S FTAPTAFRA+KREDP GE +KKYDL+  + +
Sbjct: 304 TVVYEGKPVGTPDAGAFWRMISEYKMASLFTAPTAFRAIKREDPNGELLKKYDLTGFRAL 363

Query: 362 YLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGY 421
           +LAGER+DPDTI WA+E+LKVPV+DHWWQTETGW+IAAN LG+ E P K GSP  P+PG+
Sbjct: 364 FLAGERSDPDTINWAREKLKVPVVDHWWQTETGWAIAANCLGLHEFPIKPGSPTKPVPGW 423

Query: 422 TVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGM 481
            +++LDEG  P   G++G++ V+LPLPPG L TLWNA+ R   SY + FPG Y+T DAGM
Sbjct: 424 GLEVLDEGHQPCEAGKVGSLVVRLPLPPGALLTLWNADQRCIDSYYSEFPGCYKTADAGM 483

Query: 482 KDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFL 541
            DEDGY YIM+RTDD+INVAGHRLSTG MEEVLA HPDVAECAVIGV+D LKGQ P+GF+
Sbjct: 484 IDEDGYAYIMSRTDDIINVAGHRLSTGGMEEVLASHPDVAECAVIGVADQLKGQLPLGFI 543

Query: 542 CLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGT 601
           CL AG   PH+ V+A+VVKLVREKIGPVAAFK   VV+RLPKTRSGKILRGTM  IAD  
Sbjct: 544 CLKAGVTKPHDQVIAEVVKLVREKIGPVAAFKTCTVVNRLPKTRSGKILRGTMQKIADNQ 603

Query: 602 DWKMPATIDDPAILDEITTALQGLGYAK 629
           D+KMPATIDDP+ILDEI  +L+ +GYAK
Sbjct: 604 DFKMPATIDDPSILDEIGESLESVGYAK 631


Lambda     K      H
   0.318    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: 1368
Number of extensions: 57
Number of successful extensions: 2
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: 638
Length adjustment: 38
Effective length of query: 591
Effective length of database: 600
Effective search space:   354600
Effective search space used:   354600
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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