Aligments for a candidate for hisN in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Aligments for a candidate for hisN in Shewanella loihica PV-4

Align alkaline phosphatase (EC 3.1.3.1) (characterized)
to candidate 5208648 Shew_1157 alkaline phosphatase (RefSeq)

Query= BRENDA::P00634
         (471 letters)



>lcl|FitnessBrowser__PV4:5208648 Shew_1157 alkaline phosphatase
           (RefSeq)
          Length = 545

 Score =  139 bits (350), Expect = 2e-37
 Identities = 143/489 (29%), Positives = 203/489 (41%), Gaps = 117/489 (23%)

Query: 64  AKNIILLIGDGMGDSEITAAR---NYAEGAGGFFKGI--DALPLTGQYTHYALNKKTGKP 118
           AKNIIL +GDGMG S +TAAR      +G  G    +  + LP  G    Y ++ +T   
Sbjct: 76  AKNIILFVGDGMGVSTVTAARILDGQLKGQTGEENSLSFETLPHLGLAKTYNVDGQT--- 132

Query: 119 DYVTDSAASATAWSTGVKTYNGAL----GVD------IHEKDHPTILEMAKAAGLATGNV 168
               DSA + TA  TGVKT  G +    GV+         +D  T LE+A  AG++TG V
Sbjct: 133 ---PDSAGTMTAMVTGVKTDVGVISQGEGVERGVCSSTTGQDLVTSLELAAMAGMSTGVV 189

Query: 169 STAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNAR----ADV 224
           STA +  ATPAA  AHV  R     S      P  A+  G K  I  Q+L+       +V
Sbjct: 190 STARITHATPAATYAHVPERDWEADS----NLPAEAVTNGCK-DIAAQMLDFNDGKGINV 244

Query: 225 TLGGGAKTFAETATAGEWQGK----------TLREQAQARGYQLVSDAASLNSVTEANQQ 274
            +GGG + F    T    +GK          T    AQ      V+D  S  ++ + +  
Sbjct: 245 VMGGGRRAFIPNTTVDP-EGKAGKRKDGRDLTAEWMAQYPNAAYVTDRDSFLAM-DTSTT 302

Query: 275 KPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSK 334
           +  LGLF   +M   +   +   +G                   P+LA+MT K+I++LSK
Sbjct: 303 EHALGLFNSSHMEYDYDRVEDGVNGE------------------PSLAEMTAKSIDILSK 344

Query: 335 NEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAH 394
           N+KGF L VE   ID   HA N    + +T+ L EAV+ A+E      +TL++VTADH+H
Sbjct: 345 NDKGFVLIVEAGRIDHAHHAGNAARALHDTIALSEAVRVAME-KTSANDTLLMVTADHSH 403

Query: 395 ASQIVAPDTKA---------------PGLTQALNTKDGAVMVMSYGNS------------ 427
              I    T+                P +T + +        + Y N             
Sbjct: 404 VFTIAGYPTRGNPILGLVKSNDSNGQPSVTNSTDANGMPYTTVGYANGLGFGSLETGGDE 463

Query: 428 -----------------------------EEDSQEHTGSQLRIAAYGPHAANVVGLTDQT 458
                                          +S+ H G  + I A GP A+ V G  +Q 
Sbjct: 464 RYNYAAEPGRVDLNYIDTQSAGFHQEALVPLESETHAGEDVAIFARGPGASLVEGTVEQN 523

Query: 459 DLFYTMKAA 467
            +F+ M  A
Sbjct: 524 HIFHVMNYA 532


Lambda     K      H
   0.312    0.128    0.365 

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: 673
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 471
Length of database: 545
Length adjustment: 34
Effective length of query: 437
Effective length of database: 511
Effective search space:   223307
Effective search space used:   223307
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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