Alignments for a candidate for hom in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Thiomicrospira cyclica ALM1

Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013835270.1 THICY_RS03705 homoserine dehydrogenase

Query= SwissProt::Q5F8J4
         (435 letters)



>NCBI__GCF_000214825.1:WP_013835270.1
          Length = 438

 Score =  386 bits (991), Expect = e-112
 Identities = 214/437 (48%), Positives = 289/437 (66%), Gaps = 9/437 (2%)

Query: 1   MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGR--EIRISAMCDLSEEKARQICPSA- 57
           M+P+ +G++GLGTV  G  ++L   A+    ++ +  EI+  A+ DLS  + RQ+   A 
Sbjct: 1   MQPIRLGIIGLGTVASGLVSILATQAQGSRSKIAQTFEIKKIAVRDLS--RPRQVDTGAI 58

Query: 58  AFVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPL 117
           A   DPFELV   D+DV+VEL GGT +A++ V  AI NGKHIVTANK LLA YGNE+F  
Sbjct: 59  ALTADPFELVQDPDIDVIVELMGGTTLARDLVELAIRNGKHIVTANKALLALYGNELFAQ 118

Query: 118 AEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFAD 177
           AE+Q V + FEAAVAGG+PIIKALREGL AN I  +AGIINGT N+IL++M++ G+ F  
Sbjct: 119 AEQQGVQIYFEAAVAGGVPIIKALREGLIANDIDWLAGIINGTGNYILTDMKKPGAVFEQ 178

Query: 178 VLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKY 237
           VL +AQ LGYAEADPT+D+EG DA HK+TI+++LAFG  + FS  Y EGIS++ + D+++
Sbjct: 179 VLAKAQELGYAEADPTYDVEGIDAAHKLTILASLAFGIELAFSRVYTEGISQVSADDVRF 238

Query: 238 AEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYG 297
           A+  GY IK LG+  K   G  LRVHPTL+P+  LLA V+GVMNAV V+ D VG T+ YG
Sbjct: 239 AQAFGYEIKHLGIAAKEPSGYSLRVHPTLVPKDVLLAEVNGVMNAVLVHGDQVGATMLYG 298

Query: 298 AGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQ-AQTILPMDEITSSYYLR 356
            GAG   TASAV+AD+ D+ R+ +A   H VP L    A ++ +  IL +D I + +Y+R
Sbjct: 299 PGAGGAATASAVMADLYDLGRMWQAGAEHSVPPLGRYTADLKTSANILNIDAIHTGFYVR 358

Query: 357 VQAKDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVIL---THSTVEKHIKSAIA 413
              +D PG L  I+  LA  ++SIE L Q+ +     A   +L   T+   E     A+A
Sbjct: 359 CLVEDHPGMLAAISQTLADFDISIEHLHQEPISHDNQANQALLAFTTNKVFEATFNQALA 418

Query: 414 AIEALDCVEKPITMIRM 430
            +EALD +   I  IRM
Sbjct: 419 KLEALDGMLGKINKIRM 435


Lambda     K      H
   0.318    0.135    0.369 

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: 470
Number of extensions: 22
Number of successful extensions: 4
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: 435
Length of database: 438
Length adjustment: 32
Effective length of query: 403
Effective length of database: 406
Effective search space:   163618
Effective search space used:   163618
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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