GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Azorhizobium caulinodans ORS 571

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_012172068.1 AZC_RS18230 2-isopropylmalate synthase

Query= curated2:O26819
         (496 letters)



>NCBI__GCF_000010525.1:WP_012172068.1
          Length = 526

 Score =  365 bits (937), Expect = e-105
 Identities = 215/504 (42%), Positives = 301/504 (59%), Gaps = 16/504 (3%)

Query: 2   QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61
           +V + DTTLRDGEQ PG S+T EEKL +A  ++ +G D+IEAG  I S G+ E + +I  
Sbjct: 18  RVIIFDTTLRDGEQCPGASMTFEEKLEVAELLETMGVDVIEAGFPIASIGDFESVAEIAR 77

Query: 62  EGLRAEICSFARAVREDID----AAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAV 117
               A I   +RA   DID    A        +H  + TS +H+++KL+K   +VLE  V
Sbjct: 78  RSKTAIIAGLSRAALNDIDRCAEAVKQAKRGRIHTFLSTSPVHMKYKLQKEPHQVLEMIV 137

Query: 118 DCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEF 177
                A +H   VE SAED TR++MDFL       I+AGA  I   DTVG  TP+     
Sbjct: 138 ASVTRARNHVEDVEWSAEDGTRTEMDFLCRCVEAAIKAGATTINIPDTVGYTTPQEYEAL 197

Query: 178 YRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEE 232
           +R + E       A  SVHCHND G+AVANSLAGL  GA ++  TINGIGERAGNAALEE
Sbjct: 198 FRTVRERVPNSDKAIFSVHCHNDLGMAVANSLAGLAGGARQIECTINGIGERAGNAALEE 257

Query: 233 VVVALKSLYDV---DTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADG 289
           VV+A+ +  DV    T I+  +L   S+MV+ +T   +Q NKAIVG NAFAHESGIH DG
Sbjct: 258 VVMAINTRRDVLPYRTGIDATLLTRASKMVSGVTSFPVQYNKAIVGRNAFAHESGIHQDG 317

Query: 290 VLKKAETYEPITPEMVGHGR-GFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTL 348
           +LK  +TYE +TPE VG  +   VMGKH G  A R +L  LG ++ ++ L + F R K L
Sbjct: 318 MLKHTQTYEIMTPESVGVTKTSLVMGKHSGRAAFRDKLKALGYELGENALNDAFTRFKDL 377

Query: 349 GDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTASVKLRVDDREVLEAG 408
            D  K + D D++A+ +  +    D+ V L  +++++G R    A++++ VD +  +E  
Sbjct: 378 ADRKKVIYDEDIEALVDQGIAAAYDR-VKLLSLSVIAGTRGPQRATMRIEVDGQPRIEEA 436

Query: 409 TGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGDRIISARSTQ 468
            G GPVDA   AIK  +   A   LE Y V A+T GTDA  +V ++L    ++++AR+  
Sbjct: 437 EGNGPVDATFNAIKALIPHTA--KLELYQVHAVTEGTDAQAEVSVRLAEDGKVVTARAAD 494

Query: 469 PDIIMASVEAFLSGVNRLLANEKS 492
           PD ++AS +A+++ +N+L    +S
Sbjct: 495 PDTLVASAQAYITALNKLSVKRQS 518


Lambda     K      H
   0.317    0.135    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: 631
Number of extensions: 33
Number of successful extensions: 7
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: 496
Length of database: 526
Length adjustment: 35
Effective length of query: 461
Effective length of database: 491
Effective search space:   226351
Effective search space used:   226351
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: 52 (24.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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