Alignments for a candidate for cimA in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Ferroglobus placidus DSM 10642

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_012965904.1 FERP_RS07010 2-isopropylmalate synthase

Query= BRENDA::Q58787
         (491 letters)



>NCBI__GCF_000025505.1:WP_012965904.1
          Length = 489

 Score =  504 bits (1297), Expect = e-147
 Identities = 258/491 (52%), Positives = 353/491 (71%), Gaps = 3/491 (0%)

Query: 1   MMVRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLIT 60
           M V I DTTLRDGEQTPGVSL+   KL IA+ LD LGVD+IEAG+AI S+GE + IK I+
Sbjct: 1   MSVIILDTTLRDGEQTPGVSLSVEQKLMIAEALDNLGVDIIEAGTAIASEGEFKAIKAIS 60

Query: 61  KEGLNAEICSFVRALPVDIDAALECDVDSVHLVVPTSPIHMKYKLR-KTEDEVLETALKA 119
           + GL AEICSF R    DIDAA +   DS+ +V P+S IH+  K   KT +++++ +++ 
Sbjct: 61  EAGLKAEICSFGRIKKEDIDAAADAGADSIFMVAPSSDIHINSKFPGKTREDIIQMSIEM 120

Query: 120 VEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFK 179
           VEYAKE GLIVE   EDA+R+D  F+ KL   GE+ GADR+   DTVGVLTP+++Q++  
Sbjct: 121 VEYAKERGLIVEFGGEDASRADFEFIKKLLKAGEEAGADRLTFTDTVGVLTPERAQQIMS 180

Query: 180 KITENVNLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALK 239
           ++ + V  PV+ H H+DFG+ATANT  AV GGA + H  VNG+GERAGNA+LEEVV AL+
Sbjct: 181 ELKKVVKKPVAFHGHDDFGLATANTIFAVKGGADEIHCCVNGLGERAGNAALEEVVMALE 240

Query: 240 ILYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIKNTETYE 299
            LYG  TKI  + +Y  S++V +L ++ VPPNK IVG+NAF HE+GIH   ++++ +TYE
Sbjct: 241 YLYGIKTKINKKAIYPTSKLVEKLTRVVVPPNKPIVGENAFTHESGIHTSAVLRDAKTYE 300

Query: 300 PIKPEMVGNRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGDLGKYISDA 359
           PI PE++G  R I+LGKH+G+ +++  +  +G   + EQ+ +I +RVKE GD GK ++DA
Sbjct: 301 PISPEVIGRSRSIVLGKHAGKASVEAIMKELGYKATKEQMQEILKRVKEIGDKGKRVTDA 360

Query: 360 DLLAIVREVTGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIETAYGVGPVDA 419
           D+ AI+  V     E K++L +L VVSG  I P ASVKL   G++   +E   GVGPVDA
Sbjct: 361 DVRAIIETVLQIKRERKVELVDLNVVSGANIMPTASVKLKINGKE--YVEAGVGVGPVDA 418

Query: 420 AINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVRKSDADIIRASV 479
           AINA+++A+   ADI+LV Y V+AI GGTDAL++V+V+L+KG +IV  R +  DII ASV
Sbjct: 419 AINAIKRAVKEYADIELVSYHVDAITGGTDALVDVIVQLKKGDKIVTARGARTDIIMASV 478

Query: 480 DAVMEGINMLL 490
           +A +EG+NMLL
Sbjct: 479 EAFVEGLNMLL 489


Lambda     K      H
   0.316    0.136    0.373 

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: 690
Number of extensions: 35
Number of successful extensions: 3
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: 491
Length of database: 489
Length adjustment: 34
Effective length of query: 457
Effective length of database: 455
Effective search space:   207935
Effective search space used:   207935
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 10 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